Darwin, nós temos um grande problema - as células estão repletas de padrões de design!

Design patterns of biological cells
Steven S. Andrews, H. Steven Wiley, Herbert M. Sauro
First published: 21 January 2024
https://doi.org/10.1002/bies.202300188

The central metabolic system for E. coli with highlighted regions showing several structural patterns. The metabolic map is reprinted with permission from Ref. [54].

Abstract

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

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Darwin, nós temos um problema: organismos verdes complexos surgiram há um bilhão de anos...

Phylogenomic insights into the first multicellular streptophyte 

Maaike J. Bierenbroodspot Tatyana Darienko Sophie de Vries Janine M.R. Fürst-Jansen Henrik Buschmann Thomas Pröschold Iker Irisarri Jan de Vries

Open Access Published: January 19, 2024 DOI: https://doi.org/10.1016/j.cub.2023.12.070 

Highlights

  • Comprehensive phylogenomic analyses for 38 taxonomically diverse Klebsormidiophyceae
    •   Three-order system for the Klebsormidiophyceae, resilient land colonizers
    •  Deep divergence, 830 million years ago—long before embryophytes emerged
    •  Evidence that multicellularity emerged in streptophytes about a billion years  ago

Summary 

Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1, 2, 3, 4

Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments—from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)—Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats. 5, 6

Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.

FREE PDF GRATIS: Current Biology

Novo estudo de Oxford lança luz sobre a origem dos animais

Fossilisation processes and our reading of animal antiquity

Ross P. Anderson, Christina R. Woltz, Nicholas J. Tosca, Susannah M. Porter, Derek E.G. Briggs 

Published:June 27, 2023 DOI: https://doi.org/10.1016/j.tree.2023.05.014  

Image/Imagem: Oxford University

Highlights

    The last common ancestor of animals is thought to have been small and soft-bodied and therefore would have required special conditions for its preservation.

    Limited availability of these conditions in the Neoproterozoic could explain the discrepancy between molecular clock predictions for the timing of animal origins and the fossil record of animals.

    We assess the availability of these conditions, particularly those of Burgess Shale-type, which are known to preserve animals with tissues of varied composition.

    Burgess Shale-type conditions are rarely associated with Neoproterozoic fossil biotas, but in the few assemblages with these conditions, dated to 789 million years ago or older, no animals have been identified, suggesting they had not evolved by this time.

    This provides a soft maximum age constraint on crown group animals of 789 million years ago.

Abstract

Estimates for animal antiquity exhibit a significant disconnect between those from molecular clocks, which indicate crown animals evolved ∼800 million years ago (Ma), and those from the fossil record, which extends only ∼574 Ma. Taphonomy is often held culpable: early animals were too small/soft/fragile to fossilise, or the circumstances that preserve them were uncommon in the early Neoproterozoic. We assess this idea by comparing Neoproterozoic fossilisation processes with those of the Cambrian and its abundant animal fossils. Cambrian Burgess Shale-type (BST) preservation captures animals in mudstones showing a narrow range of mineralogies; yet, fossiliferous Neoproterozoic mudstones rarely share the same mineralogy. Animal fossils are absent where BST preservation occurs in deposits ≥789 Ma, suggesting a soft maximum constraint on animal antiquity.

Keywords Burgess Shale-type clays molecular clocks Neoproterozoic Era origin of animals 

FREE PDF GRATIS: Trends in Ecology & Evolution

Darwin, os lagos rasos de soda são promissores como berços da vida na Terra

Biogeochemical explanations for the world’s most phosphate-rich lake, an origin-of-life analog

Sebastian Haas, Kimberly Poppy Sinclair & David C. Catling

Communications Earth & Environment volume 5, Article number: 28 (2024) 

 

Last Chance Lake in western Canada in November 2021, when the lake has shrunk into many smaller pools and ice has formed on top of each pool.

Kimberly Poppy Sinclair/University of Washington

Abstract

Environmental phosphate concentrations are typically much lower (~10⁻⁶ M) than needed for prebiotic phosphorylation of nucleosides, critical for the origin of life. Here, we tested hypotheses explaining highly concentrated dissolved phosphate in carbonate-rich “soda” lakes by examining phosphorus and nitrogen cycling in Last Chance Lake and Goodenough Lake, Canada. We find a lack of geochemical phosphorus precipitation, that sedimentary calcium is in dolomite rather than apatite, and that N₂-fixation rates, probably suppressed by high salinity, are too low to create significant biological phosphate demand. Thus, nitrogen-limitation of biological production and precipitation of calcium-rich carbonate instead of apatite combine to allow unimpeded evaporative phosphate buildup in Last Chance Lake to the highest known natural levels (37 mM) due to small biological and geochemical phosphorus sinks. Forming on basaltic rock, which was likely common on early Earth, evaporative soda lakes were consequently plausible origin-of-life settings with sufficient phosphate for prebiotic synthesis.

FREE PDF GRATIS:  Communications Earth & Environment Sup. Info. Peer Rev File

Novas evidências contra a ancestralidade dos dinossauros nas aves

Sexta-feira de fóssil: novas evidências contra a ancestralidade dos dinossauros nas aves 

 

Günter Bechly

5 de janeiro de 2024, 6h45 

 

Nesta Sexta-feira de Fóssil revisitamos a ancestralidade dos pássaros, com o esqueleto da ave do Cretáceo Superior Hesperornis gracilis, exibido no Museu de História Natural de Karlsruhe, Alemanha. Hesperornis era uma ave marinha que não voava e com dentes, um tanto semelhante aos pinguins modernos, e viveu na época de alguns dos dinossauros raptores bem conhecidos dos filmes Jurassic Park.

 

Poucas hipóteses na biologia evolutiva se tornaram tão populares entre os leigos quanto a postulada ancestralidade dos pássaros a partir dos dinossauros bípedes. Na verdade, muitas crianças em idade escolar dirão com orgulho que os pássaros são simplesmente dinossauros sobreviventes. A ancestralidade terópode das aves tornou-se um dogma evolutivo que é quase universalmente aceito e ensinado como visão consensual. No entanto, existem alguns dissidentes, entre os quais o paleornitólogo Alan Feduccia, da Universidade da Carolina do Norte, é certamente o mais proeminente. Ele cunhou o famoso termo “paradoxo temporal” para o fato de que o registro fóssil do suposto grupo de aves terópodes tende a ser mais jovem do que as aves reais mais antigas. Na semana passada discuti novas evidências que tornam este paradoxo temporal muito pior (Bechly 2023).

 

Além do registro fóssil

Contudo, a crítica de Feduccia à hipótese dinossauro-pássaro não se baseia apenas em problemas com o registo fóssil, mas também em evidências contraditórias da anatomia comparativa. Agora, ele apresenta novas evidências que contradizem ainda mais nitidamente a visão consensual. Um dos argumentos para uma relação dinossauro-pássaro tem sido a presença do chamado acetábulo “aberto”, que “é uma superfície pélvica côncava formada pelo ílio, ísquio e púbis, que acomoda a cabeça do fêmur nos tetrápodes”. .” Feduccia (2024) estudou o acetábulo em aves basais precoces e descobriu que seu acetábulo tende a ser parcialmente fechado e um antitrocânter (processo do ísquio ou ilíaco) está ausente.Isto põe fortemente em dúvida um dos personagens-chave para uma relação dinossauro-pássaro e sugere que esta hipótese deve ser reavaliada. O fato de que microraptorídeos e troodontídeos “também exibem fechamento parcial do acetábulo e não possuem um antitrocânter é mais uma incongruência, pois esses táxons deveriam exibir modificações “típicas” da cintura pélvica de terópodes para cursorialidade terrestre”. Isto poderia apoiar a opinião de vários especialistas (por exemplo, Martin 2004, e vários estudos citados por Feduccia), de que estes táxons maniraptoranos representam aves secundariamente incapazes de voar, em vez de dinossauros terópodes.

 

Feduccia concluiu seu novo estudo com esta declaração notável:

"A hipótese de que as aves são dinossauros terópodes maniraptoranos, apesar da certeza com que é proclamada, continua a sofrer de dificuldades não resolvidas… Até problemas como os aqui discutidos — e muitos outros que continuam a ser descartados quer por apelo ao “consenso” quer por excesso de confiança nos resultados da análise filogenética de dados morfológicos - foram resolvidos satisfatoriamente, o ceticismo em relação ao consenso atual e a investigação contínua de hipóteses alternativas são necessários para a promoção do discurso crítico na filogenética dos vertebrados e na biologia evolutiva."

 

Afinal, pássaros e dinossauros podem não representar pedaços arbitrários de um grau evolutivo, mas podem, em vez disso, representar tipos naturais distintos. No mínimo, as evidências parecem ser muito mais ambíguas, mais fracas e menos convincentes do que a maioria dos biólogos evolucionistas gosta de fingir.
 

Referências

 

BECHLY G 2023. Fossil Friday: Fossil Bird Tracks Expand the Temporal Paradox. Evolution News December 29, 2023. https://evolutionnews.org/2023/12/fossil-friday-fossil-bird-tracks-expand-the-temporal-paradox/
 

FEDUCCIA A 2024. The Avian Acetabulum: Small Structure, but Rich with Illumination and Questions. Diversity 16: 20, 1–28. DOI: https://doi.org/10.3390/d16010020 

 

MARTIN LD 2004. A basal archosaurian origin for birds. Acta Geologica Sinica 50(6), 978–990. https://caod.oriprobe.com/articles/7989071/A_basal_archosaurian_origin_for_birds.htm

 

 

 

GÜNTER BECHLY 

Membro Sênior, Centro de Ciência e Cultura

Günter Bechly é um paleoentomologista alemão especializado na história fóssil e na sistemática de insetos (especialmente libélulas), o mais diverso grupo de animais. Ele atuou como curador de âmbar e fósseis de insetos no departamento de paleontologia do Museu Estadual de História Natural (SMNS) em Stuttgart, Alemanha. Ele também é membro sênior do Centro de Ciência e Cultura do Discovery Institute. Dr. Bechly obteve seu Ph.D. em geociências pela Eberhard-Karls-University em Tübingen, Alemanha.

Veja papai, veja mamãe, sem mitocondria!!!

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

Lukáš V. F. Novák, Sebastian C. Treitli, Jan Pyrih, Paweł Hałakuc, Shweta V. Pipaliya, Vojtěch Vacek, Ondřej Brzoň, Petr Soukal, Laura Eme, Joel B. Dacks, Anna Karnkowska, Marek Eliáš,     Vladimír Hampl

PLOS Published: December 7, 2023

https://doi.org/10.1371/journal.pgen.1011050

 

A protist - Dan Wieczynski

Abstract

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.

Author summary

Mitochondria are nearly ubiquitous components of eukaryotic cells that constitute bodies of animals, fungi, plants, algae, and a broad diversity of single-celled eukaryotes, a.k.a. protists. Many groups of protists have substantially reduced the complexity of their mitochondria because they live in oxygen-poor environments, so they are unable to utilize the most salient feature of mitochondria–their ATP-producing oxidative phosphorylation metabolism. However, for a long time, scientists thought that it is impossible to completely lose a mitochondrion because this organelle provides other essential services to the cell, e.g. synthesis of protein cofactors called iron-sulfur clusters. Detailed investigation of the chinchilla symbiont M. exilis documented the first case of an organism without mitochondrion, and it also provided a scenario explaining how this unique evolutionary experiment might have happened. In this work, we expand on this discovery by exploring genomes of multiple relatives of M. exilis. We show that the loss of the mitochondrion is not limited to a single species but possibly extends to its entire group, the oxymonads. We also compare the predicted metabolic capabilities of oxymonads to their closest known mitochondrion-containing relatives and map out various changes that occurred during the transition to amitochondriality.

FREE PDF: PLoS Genetics