Edward Hitchcock’s Pre-Darwinian (1840) “Tree of Life”

The “tree of life” iconography, representing the history of life, dates from at least the latter half of the 18th century, but evolution as the mechanism providing this bifurcating history of life did not appear until the early 19th century. There was also a shift from the straight line, scala naturae view of change in nature to a more bifurcating or tree-like view. Throughout the 19th century authors presented tree-like diagrams, some regarding the Deity as the mechanism of change while others argued for evolution. Straight-line or anagenetic evolution and bifurcating or cladogenetic evolution are known in biology today, but are often misrepresented in popular culture, especially with anagenesis being confounded with scala naturae. Although well known in the mid 19th century, the geologist Edward Hitchcock has been forgotten as an early, if not the first author to publish a paleontologically based “tree of life” beginning in 1840 in the first edition of his popular general geology text Elementary Geology. At least 31 editions were published and those between 1840 and 1859 had this “paleontological chart” showing two trees, one for fossil and living plants and another for animals set within a context of geological time. Although the chart did not vary in later editions, the text explaining the chart did change to reflect newer ideas in paleontology and geology. Whereas Lamarck, Chambers, Bronn, Darwin, and Haeckel saw some form of transmutation as the mechanism that created their “trees of life,” Hitchcock, like his contemporaries Agassiz and Miller, who also produced “trees of life,” saw a deity as the agent of change. Through each edition of his book Hitchcock denounced the newer transmutationist hypotheses of Lamarck, then Chambers, and finally Darwin in an 1860 edition that no longer presented his tree-like “paleontological chart.”     

小麦族鹅观草属三个物种的关系研究

通过形态学特征比较、种间杂交、染色体组配对和繁育学资料,探讨鹅观草属拟披碱草组纤毛草系中的三个物种毛叶鹅观草、纤毛鹅观草和竖立鹅观草间的亲缘关系。结果表明毛叶鹅观草与纤毛鹅观草、竖立鹅观草存在一定的生殖障碍,纤毛鹅观草和竖立鹅观草不存在生殖障碍。建议将毛叶鹅观草作为纤毛鹅观草的亚种,而竖立鹅观草作为纤毛鹅观草的变种处理较为适宜。     

Irreversibly glycated LDL induce oxidative and inflammatory state in human endothelial cells; added effect of high glucose

In diabetes, hyperglycemia and the associated formation of advanced glycation end-products (AGE) and AGE-modified low density lipoproteins (AGE-LDL) can directly affect the cells of the vascular wall. We hypothesize that AGE-LDL may act directly and induce oxidant and inflammatory alterations in human endothelial cells (HEC), this effect being amplified by high glucose. To test this assumption, the activity of NADPH oxidase (NADPHox) was evaluated and the expression of its subunits (p22^phox, NOX4, and p67^phox), of the AGE receptor (RAGE), and of the monocyte chemoattractant protein-1 (MCP-1) were assessed by real-time PCR and Western blot in confluent EA.hy926 cells incubated with AGE-LDL for 24 and 48 h, in normal and high glucose conditions. Exposure of HEC for 48 h to AGE-LDL in 5 mM glucose induced an increase of RAGE expression (50%), NADPHox activity (107%), p22^phox and NOX4 mRNA (50% and 188%, respectively) and MCP-1 expression (80%). AGE-LDL-stimulated p22^phox expression by activating p38 MAP kinase and NF-kB, and MCP-1 expression by activating NF-kB, as demonstrated by the use of specific inhibitors (SB203580 and Bay11-7085). The addition of 25 mM glucose in the culture medium enhanced the effect of AGE-LDL, but also of nLDL, on RAGE, p22^phox, NOX4, p67^phox, and MCP-1 gene expression. In conclusion, AGE-LDL induce an oxidative stress and a pro-inflammatory state in human endothelial cells. Both AGE-LDL and nLDL in the presence of high glucose amplify their effect, revealing a link between hyperlipidemia, diabetes, and endothelial cell dysfunction.     

Molecular Insights into the Interaction between α-Synuclein and Docosahexaenoic Acid

α-Synuclein (α-syn) is a 140-residue protein of unknown function, involved in several neurodegenerative disorders, such as Parkinson's disease. Recently, the possible interaction between α-syn and polyunsaturated fatty acids has attracted a strong interest. Indeed, lipids are able to trigger the multimerization of the protein in vitro and in cultured cells. Docosahexaenoic acid (DHA) is one of the main fatty acids (FAs) in cerebral gray matter and is dynamically released following phospholipid hydrolysis. Moreover, it has been found in high levels in brain areas containing α-syn inclusions in patients affected by Parkinson's disease. Debated and unsolved questions regard the nature of the molecular interaction between α-syn and DHA and the effect exerted by the protein on the aggregated state of the FA. Here, we show that α-syn is able to strongly interact with DHA and that a mutual effect on the structure of the protein and on the physical state of the lipid derives from this interaction. α-Syn acquires an α-helical conformation in a simple two-state transition. The binding of the protein to the FA leads to a reduction of the size of the spontaneously formed aggregated species of DHA as well as of the critical aggregate concentration of the lipid. Specifically, biophysical methods and electron microscopy observations indicated that the FA forms oil droplets in the presence of α-syn. Limited proteolysis experiments showed that, when the protein is bound to the FA oil droplets, it is initially cleaved in the 89-102 region, suggesting that this chain segment is sufficiently flexible or unfolded to be protease-sensitive. Subsequent proteolytic events produce fragments corresponding to the first 70-80 residues that remain structured and show high affinity for the lipid. The fact that a region of the polypeptide chain remains accessible to proteases, when interacting with the lipid, suggests that this region could be involved in other interactions, justifying the ambivalent propensity of α-syn towards folding or aggregation in the presence of FAs.     

Dissection of the DNA Mimicry of the Bacteriophage T7 Ocr Protein using Chemical Modification

The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an ∼ 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove ∼ 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to ∼ 800-fold.     

The GroEL/GroES cis cavity as a passive anti-aggregation device

The GroEL/GroES chaperonin folding chamber is an encapsulated space of ∼65 Å diameter with a hydrophilic wall, inside of which many cellular proteins reach the native state. The question of whether the cavity wall actively directs folding reactions or is playing a passive role has been open. We review past and recent observations and conclude that the chamber functions as a passive “Anfinsen cage” that prevents folding monomers from multimolecular aggregation.     

Proteomic analysis of lipid raft-enriched membranes isolated from internal organelles

The mitochondria-associated membrane (MAM) is a sub-region of the endoplasmic reticulum (ER) that facilitates crosstalk between the ER and mitochondria. The MAM actively influences vital cellular processes including Ca²⁺ signaling and protein folding. Detergent-resistant microdomains (DRMs) may localize proteins to the mitochondria/MAM interface to coordinate these events. However, the protein composition of DRMs isolated from this region is not known. Lipid-raft enriched DRMs were isolated from a combined mitochondria/MAM sample and analyzed using two-dimensional reversed-phased tandem mass spectrometry. Strict post-acquisition filtering of the acquired data led to the confident identification 250 DRM proteins. The majority (58%) of the identified proteins are bona fide mitochondrial or ER proteins according to Gene Ontology annotation. Additionally, 74% of the proteins have previously been noted as MAM-resident or -associated proteins. Furthermore, ∼20% of the identified proteins have a documented association with lipid rafts. Most importantly, known internal LR marker proteins (inositol 1,4,5-trisphosphate receptor type 3, erlin-2, and voltage-dependent anion channel 1) were detected as well as most of the components of the mitochondrial/MAM-localized Ca²⁺ signaling complex. Our study provides the basis for future work probing how the protein activities at the mitochondrion/MAM interface are dependent upon the integrity of these internal lipid-raft-like domains.