Mystery at the heart of life

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December 21, 2014

Cell biology, Intelligent Design, News

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Cell biology
Intelligent Design
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By Biologic Institute’s Ann Gauger, at Christianity Today’s Behemoth, the secret life of cells:

Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

How they work together so optimally and efficiently is not merely amazing, but also a great enigma, a mystery that lies at the heart of life itself. More. Paywall soon after. May be worth it.

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We further performed multiphoton imaging to observe very deep structures of epithelial cells that were not observed in conventional confocal microscopy. To our surprise, we found very long vertical structures of epithelial cells down to 130 ?m in the case of J. orithya. Interestingly, some elongated structures were “clustered” or “bundled” at a certain depth. These cellular clusters may be a unit of differentiation. Another surprising finding was the possible discovery of horizontal bridges that connect two clusters of epithelial tails
Ohno Y, Otaki JM (2015) Live Cell Imaging of Butterfly Pupal and Larval Wings In Vivo. PLoS ONE 10(6): e0128332. doi:10.1371/journal.pone.0128332 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128332

Surprised? why? did they expect something else? Interesting? duh! that's a gross understatement... most of what we see in biology is beyond fascinating! :) Possible discovery? why possible? not sure about it yet? :) Of course, more advanced technology will reveal fascinating things that were not seen with current technology. The deeper they will be able to look into the elaborate cellular and molecular functional information-processing choreographies orchestrated within the biological systems, the more surprising, shocking, unexpected, unanticipated, mind-boggling things they will find, unless they finally start thinking out of their dogmatic box, with open-minded attitude, with the innocent sense of wonder of a child, enjoying in awe the unending revelation of the Ultimate Reality. Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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It is interesting to note that some hemocytes were physically close to (probably in contact with) epithelial cells. We speculate that these hemocytes (i.e., macrophage-like cells) are eliminating apoptotic epithelial cells.
Ohno Y, Otaki JM (2015) Live Cell Imaging of Butterfly Pupal and Larval Wings In Vivo. PLoS ONE 10(6): e0128332. doi:10.1371/journal.pone.0128332 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128332

Speculate? hmmm... Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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We believe that these seemingly overlapping patterns are not dye-dependent, but they arise because of the highly intermingled packaging of mitochondria, ER, and cytoplasm. We believe that this dramatic morphological transformation of epithelial cells is likely accompanied by functional changes. We believe that calcium waves travel more shallow positions [...] We believe, [...] that cell size and shape may be determined by positional information, which may be identical to a ploidy signal
Ohno Y, Otaki JM (2015) Live Cell Imaging of Butterfly Pupal and Larval Wings In Vivo. PLoS ONE 10(6): e0128332. doi:10.1371/journal.pone.0128332 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128332

We believe... evidence-based faith? Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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We do not know if this heterogeneity results from technical difficulty for even staining or from biochemical heterogeneity of endosome-like or autophagosome-like bodies. Time-lapse long-term imaging at the cellular level is a challenge in the future. More systematic characterization of the Z. maha system and its comparison to the J. orithya system are expected in the future. In the future, combinations of these methods will allow us to manipulate molecules inside the epithelium and to monitor changes in living pupal wing cells in vivo.
Ohno Y, Otaki JM (2015) Live Cell Imaging of Butterfly Pupal and Larval Wings In Vivo. PLoS ONE 10(6): e0128332. doi:10.1371/journal.pone.0128332 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128332

in the future... in the future... in the future... Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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Butterfly wing color patterns are determined during the late larval and early pupal stages. Characterization of wing epithelial cells at these stages is thus critical to understand how wing structures, including color patterns, are determined.
Ohno Y, Otaki JM (2015) Live Cell Imaging of Butterfly Pupal and Larval Wings In Vivo. PLoS ONE 10(6): e0128332. doi:10.1371/journal.pone.0128332 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128332

Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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[...] spontaneous Ca 2+ waves play critical roles in scale development and color pattern formation, which are involved in two-dimensional morphogenesis in butterfly wings. The mechanism that underlies the intercellular propagation of Ca 2+ waves is currently unknown. The relationship between Ca 2+ waves and the predicted ultra-slow waves remains to be clarified. To demonstrate a direct functional role of Ca 2+ waves in wing development, genetic manipulations may be required in the future.
Spontaneous long-range calcium waves in developing butterfly wings Yoshikazu Ohno and Joji M Otaki BMC Developmental Biology, 15:17 doi:10.1186/s12861-015-0067-8 http://www.biomedcentral.com/1471-213X/15/17

Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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It is unclear whether the short-term effects of thapsigargin eventually led to long-term phenotypic effects without any side effects. In other words, we do not know whether its effects on cover scales are direct or indirect results of the abolishment of Ca 2+ waves. However, we speculate that [...]
Spontaneous long-range calcium waves in developing butterfly wings Yoshikazu Ohno and Joji M Otaki BMC Developmental Biology, 15:17 doi:10.1186/s12861-015-0067-8 http://www.biomedcentral.com/1471-213X/15/17

speculate ? hmmm... Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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[...] spontaneous Ca 2+ waves coordinate [?] cellular processes, including morphogenesis during development. The waves appear to be generated [?] from cells of morphological importance in the developing neocortex, such as S-phase cells [...] A more detailed morphological characterization of epithelial cells is currently underway in our laboratory.
Spontaneous long-range calcium waves in developing butterfly wings Yoshikazu Ohno and Joji M Otaki BMC Developmental Biology, 15:17 doi:10.1186/s12861-015-0067-8 http://www.biomedcentral.com/1471-213X/15/17

Coordinate? how? Generated? why? how? Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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[...] the present study is mainly descriptive, and a direct functional role of Ca 2+ waves cannot be rigorously proven by these methods because many other molecular pathways may be modified by physical damage and chemical injections, which could then indirectly change scale morphology and color patterns in the long term.
Spontaneous long-range calcium waves in developing butterfly wings Yoshikazu Ohno and Joji M Otaki BMC Developmental Biology, 15:17 doi:10.1186/s12861-015-0067-8 http://www.biomedcentral.com/1471-213X/15/17

mainly descriptive? Well, what else is new? Many papers (specially on the "evo-devo" daydreaming hogwash) are mainly (or partially in the best cases) boring passive descriptions, lacking thoroughly rigorous detailed molecular proofs of the functional information-processing processes they attempt to describe so poorly. Complex complexity. Work in progress... stay tuned.Dionisio_{October 19, 2015
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For many waves, we were unable to find a clear point of origin or trajectory. We believe that this was largely because our visual field was not large enough to find originating points for the waves.
Spontaneous long-range calcium waves in developing butterfly wings Yoshikazu Ohno and Joji M Otaki BMC Developmental Biology, 15:17 doi:10.1186/s12861-015-0067-8 http://www.biomedcentral.com/1471-213X/15/17

Believe? Evidence-based faith? :) Complex complexity. Work in progress... stay tuned.Dionisio_{October 18, 2015
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[...] developmental time is affected by temperatures via hormonal changes. Similar hormonal factors may be responsible for forewing size [...] [...] these factors will be examined in the future [...] [...] it has been proposed that temperature-related hormones [...] function in [...] to determine wing color patterns. Their potential functions in body size determination await further study. Plastic expression of color patterns and wing size may be coordinated developmentally by cell proliferation to adjust the number of cells and by cell growth to adjust cell size. [...] body size rules and their associated discussion in biology are often oversimplified based on fragmentary results. [...] forewing size was shown to be dependent on rearing temperatures [...]
Body size distributions of the pale grass blue butterfly in Japan: Size rules and the status of the Fukushima population Wataru Taira, Mayo Iwasaki & Joji M. Otaki Scientific Reports 5, Article number: 12351 doi:10.1038/srep12351 http://www.nature.com/articles/srep12351

Complex complexity. Work in progress... stay tuned.Dionisio_{October 18, 2015
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[...] a number of key questions remain to be answered [...] it is essential to explore the cellular and molecular characteristics of specialized filopodia to provide novel insight into their formation and how they establish precise orientations and lengths within diverse cellular landscapes. [...] we know little about the molecular players involved in the transport of signaling molecules along specialized filopodia, including control of their speeds and directional movement. [...] we do not know how the localization of signaling molecules along filopodia establishes the formation of a concentration gradient.
Specialized filopodia: at the ‘tip’ of morphogen transport and vertebrate tissue patterning Corinne L Fairchild, Maria Barna Current Opinion in Genetics & Development Volume 27, Pages 67–73 Developmental mechanisms, patterning and evolution http://www.sciencedirect.com/science/article/pii/S0959437X14000203

Complex complexity. Work in progress... stay tuned.Dionisio_{October 18, 2015
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[...] how do signaling molecules travel through intricate embryonic tissues, over impressive distances, and along complex cellular landscapes to reach responding cells? How are embryonic cells able to precisely establish morphogen concentration gradients required to dictate unique cell fates and behaviors?
Specialized filopodia: at the ‘tip’ of morphogen transport and vertebrate tissue patterning Corinne L Fairchild, Maria Barna Current Opinion in Genetics & Development Volume 27, Pages 67–73 Developmental mechanisms, patterning and evolution http://www.sciencedirect.com/science/article/pii/S0959437X14000203

Complex complexity. Work in progress... stay tuned.Dionisio_{October 18, 2015
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For over a century, biologists have strived to unravel the mechanisms that establish how cells are informed of their position in the embryo and differentiate to give rise to complex organs and structures. However, the historical idea that one predominant mode of ligand transport, largely accounted for by free diffusion, can explain how all signaling molecules, known as morphogens, control tissue patterning has greatly hindered our ability to fully appreciate the complexities driving the delivery and reception of signaling molecules at a distance. In reality, a cell’s shape, morphology, and location change continuously as development progresses. Thus, cellular context poses distinct challenges for morphogen transport in each unique cellular environment. Emerging studies reveal that some cells overcome such obstacles in an unexpected manner: via long, cellular projections, or specialized filopodia, that link distant cells and traffic signaling components.
Specialized filopodia: at the ‘tip’ of morphogen transport and vertebrate tissue patterning Corinne L Fairchild, Maria Barna Current Opinion in Genetics & Development Volume 27, Pages 67–73 Developmental mechanisms, patterning and evolution http://www.sciencedirect.com/science/article/pii/S0959437X14000203

historical idea [...] has greatly hindered our ability to fully appreciate the complexities [...] ? What kind of 'historical' idea was that? Reductionist ? Aren't scientists supposed to be open-minded and think out of the box? unexpected manner? Why unexpected? Did they expect anything in particular? Complex complexity. Work in progress... stay tuned.Dionisio_{October 18, 2015
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[...] optimal LN scanning results from a combination of the intrinsic migratory versatility of T cells, the local chemokine milieu and the intricate microarchitecture of the LN. The remarkable ability of T lymphocytes to switch from one migration mode to another is underpinned by a complex cross-talk of signalling pathways, of which the small GTPases of the Rho and Rap family are central. The next challenge, however, will be the complete mapping of these signalling cascades, and a better understanding of the variations in the regulation and function of these pathways among different T cell subsets.
T cell migration in intact lymph nodes in vivo Marcia A Munoz, Maté Biro, Wolfgang Weninger Current Opinion in Cell Biology Volume 30, Pages 17–24 Cell adhesion and migration http://www.sciencedirect.com/science/article/pii/S0955067414000556

Complex complexity. Work in progress... remain tuned.Dionisio_{October 18, 2015
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How such gradients present and act in the context of an organism is far less clear. [...] what cells actually do in complex living organisms is far less clear. [...] the molecular complexity hidden behind the observed process is often underestimated. [...] the spatial and temporal dynamics of gradient formation, propagation and interpretation remain largely unknown in physiological contexts. [...] the inclusion of more complex behaviors in modeling studies will help shed light into the ability of cells to decipher intricate in vivo environments.
NEW PARADIGMS IN THE ESTABLISHMENT AND MAINTENANCE OF GRADIENTS DURING DIRECTED CELL MIGRATION Ritankar Majumdar, Michael Sixt, and Carole A. Parent Curr Opin Cell Biol. 0: 33–40. doi: 10.1016/j.ceb.2014.05.010 http://www.sciencedirect.com/science/article/pii/S0955067414000635

Complex complexity. Work in progress... remain tuned.Dionisio_{October 18, 2015
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Pathogenesis of the NAFLD is a very complex process and may have many mechanisms. Carotenoids, which are antioxidant natural compounds, appear to have beneficial effects in the prevention and treatment of NAFLD. Antioxidant and anti-inflammatory properties are the leading mechanisms of actions of carotenoids. These effects modulate intracellular signaling pathways influencing gene expression and protein translation. Future investigations are warranted to understand the precise mechanisms as well as potential preventive and therapeutic effects of carotenoids in NAFLD and HCC.
Carotenoids and NAFLD doi: 10.3978/j.issn.2304-3881.2015.01.11 http://www.thehbsn.org/article/view/5850/7324

Had we remained in Eden, NAFLD wouldn't have been an issue at all. But we preferred to do things our way.Dionisio_{October 17, 2015
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[...] further research into the role of egg intake on immunity is warranted.
Bioactive Egg Components and Inflammation Catherine J. Andersen Nutrients 2015, 7(9), 7889-7913; doi:10.3390/nu7095372 http://www.mdpi.com/2072-6643/7/9/5372/htm

Interesting.Dionisio_{October 17, 2015
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[...] we should start to integrate the impact on intestinal microbiota composition and subsequent inflammatory responses in the nutritional value of foods, as a proxy for predicting the potential to evoke dysmetabolic states that are determinants of NAFLD development.
Nádia Duarte, Inês C. Coelho, Rita S. Patarrão, Joana I. Almeida, Carlos Penha-Gonçalves, and M. Paula Macedo, “How Inflammation Impinges on NAFLD: A Role for Kupffer Cells,” BioMed Research International, vol. 2015, Article ID 984578, 11 pages, 2015. doi:10.1155/2015/984578

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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[...] it is clear that much remains to be understood regarding the mechanism of the disease. The lack of knowledge in relation to this pathogenesis becomes a hurdle in the path towards novel approaches for the prevention and treatment of the disease. How the interdependent effects of diet microbiota inflammation directly impact liver dysmetabolism is an issue that remains to be elucidated.
Nádia Duarte, Inês C. Coelho, Rita S. Patarrão, Joana I. Almeida, Carlos Penha-Gonçalves, and M. Paula Macedo, “How Inflammation Impinges on NAFLD: A Role for Kupffer Cells,” BioMed Research International, vol. 2015, Article ID 984578, 11 pages, 2015. doi:10.1155/2015/984578

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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NAFLD is rapidly becoming the most prevalent cause of liver disease worldwide and afflicts adults and children as currently associated with obesity and insulin resistance. Even though lately some advances have been made to elucidate the mechanism and causes of the disease much remains unknown about NAFLD.
Nádia Duarte, Inês C. Coelho, Rita S. Patarrão, Joana I. Almeida, Carlos Penha-Gonçalves, and M. Paula Macedo, “How Inflammation Impinges on NAFLD: A Role for Kupffer Cells,” BioMed Research International, vol. 2015, Article ID 984578, 11 pages, 2015. doi:10.1155/2015/984578

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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Further studies deciphering the cellular source, targets and signalling components of exercise-induced EVs are required to reveal their potential role as mediators of health-promoting effects associated with physical activity.
Physical exercise induces rapid release of small extracellular vesicles into the circulation Journal of Extracellular Vesicles 2015, 4: 28239 - http://dx.doi.org/10.3402/jev.v4.28239

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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Future studies may help to establish how widespread the phenomenon of EV-mediated cross-kingdom communication is. [...] in further developing the great scope of physiological cell system compositions and dynamics – previously understood to be comprised of different tissue stroma, body fluids and soluble mediators – the presence and functional modalities of EVs should now be considered and paradigms redefined. The biology of EVs – their molecular composition and function, targeting and uptake mechanisms – is still a young research field, to some extent awaiting new technological advances for the isolation and characterization of complex mixtures including very small vesicles. More extensive research to establish a deeper understanding of the physiological relevance of EVs in different homeostatic changes is now warranted.
Biological properties of extracellular vesicles and their physiological functions Journal of Extracellular Vesicles 2015, 4: 27066 - http://dx.doi.org/10.3402/jev.v4.27066

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids [...] [...] the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored.
Biological properties of extracellular vesicles and their physiological functions Journal of Extracellular Vesicles 2015, 4: 27066 - http://dx.doi.org/10.3402/jev.v4.27066

Complex complexity. Work in progress... stay tuned.Dionisio_{October 16, 2015
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It has been said that nothing requires an architect’s care more than “due proportions.” What is true of buildings is also true of bodies, though the means by which bodies achieve their proportions are rather more mysterious than an architect’s whims. With bodies, much depends on genes, gene expression, and the localization and diffusion gradients of gene products called morphogens.
GEN News Highlights Body Proportions Go Back to the Egg … and Its Ration of Maternal Resources http://www.genengnews.com/gen-news-highlights/body-proportions-go-back-to-the-egg-and-its-ration-of-maternal-resources/81251081/

Complex complexity.Dionisio_{October 14, 2015
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[...] scaling of the ?Bcd gradient in the embryo originates from, and is constrained fundamentally by, a dynamic relationship between maternal tissue expansion and ?bcd gene copy number expansion in the ovary.
Fundamental origins and limits for scaling a maternal morphogen gradient Feng He, Chuanxian Wei, Honggang Wu, David Cheung, Renjie Jiao & Jun Ma Nature Communications 6, Article number: 6679 doi:10.1038/ncomms7679 http://www.nature.com/ncomms/2015/150326/ncomms7679/full/ncomms7679.html

Complex complexity. Work in progress... stay tuned.Dionisio_{October 14, 2015
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Tissue expansion and patterning are integral to development; however, it is unknown quantitatively how a mother accumulates molecular resources to invest in the future of instructing robust embryonic patterning.
Fundamental origins and limits for scaling a maternal morphogen gradient Feng He, Chuanxian Wei, Honggang Wu, David Cheung, Renjie Jiao & Jun Ma Nature Communications 6, Article number: 6679 doi:10.1038/ncomms7679 http://www.nature.com/ncomms/2015/150326/ncomms7679/full/ncomms7679.html

Complex complexity. Work in progress... stay tuned.Dionisio_{October 14, 2015
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[...] the combination of quantitative smFISH data and mathematical modelling can be a powerful tool to dissect the dynamics of signalling pathways in development.
Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression Jeroen Sebastiaan van Zon, Simone Kienle, Guizela Huelsz-Prince, Michalis Barkoulas & Alexander van Oudenaarden Nature Communications 6, Article number: 7053 doi:10.1038/ncomms8053 http://www.nature.com/ncomms/2015/150511/ncomms8053/full/ncomms8053.html

Complex complexity. Work in progress... stay tuned.Dionisio_{October 14, 2015
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[...] during vulva induction downstream gene expression is not controlled exclusively by the external LIN-3 gradient and lateral Notch inhibition but also by the intrinsic modulation of the downstream signal by the receiving cells.
Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression Jeroen Sebastiaan van Zon, Simone Kienle, Guizela Huelsz-Prince, Michalis Barkoulas & Alexander van Oudenaarden Nature Communications 6, Article number: 7053 doi:10.1038/ncomms8053 http://www.nature.com/ncomms/2015/150511/ncomms8053/full/ncomms8053.html

Complex complexity. Work in progress... stay tuned.Dionisio_{October 14, 2015
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[...] the observed dynamic changes in sensitivity point to a so far unrecognized temporal aspect of the response to the external LIN-3 signal. It would be interesting to examine whether the change in sensitivity to LIN-3 of Notch ligand induction is part of a larger temporal programme. [...] it might be possible that other genes expressed in 1° fate cells, including other Ras targets, might show concomitant changes in expression.
Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression Jeroen Sebastiaan van Zon, Simone Kienle, Guizela Huelsz-Prince, Michalis Barkoulas & Alexander van Oudenaarden Nature Communications 6, Article number: 7053 doi:10.1038/ncomms8053 http://www.nature.com/ncomms/2015/150511/ncomms8053/full/ncomms8053.html

It might be possible that [...] might show [...] Sounds very 'mighty', doesn't it? ;) Complex complexity. Work in progress... stay tuned.Dionisio_{October 14, 2015
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