The NCBI Databases: an Evolutionist’s Perspective

The National Center for Biotechnology Information (NCBI) organizes information resources for life scientists on an evolutionary scheme. This facilitates research about present-day organisms. The recent discovery of a new arenavirus, the LUJO virus, illustrates the utility of adopting evolution as a central architectural principle for life sciences databases: using the NCBI’s resources, clinicians were able to classify the new virus in real time—soon enough to aid in the diagnosis and treatment of a hemorrhagic fever caused by the LUJO virus. Topics fundamental to the study of evolution, often thought of as useless, are indeed vital because they inform how life science information ought to be organized.     

The mechanism of oxidation-induced low-density lipoprotein aggregation: an analogy to colloidal aggregation and beyond?

Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein molecules aggregate and form nucleation units. The nucleation units chain together and form linear aggregates. The linear aggregates branch and interact with one another, forming fractals. In the fusion stage, spatially adjacent nucleation units in the fractal fuse into curved membrane surfaces, which, in turn, fuse into multilamellar or unilamellar vesicles. Alternatively, some adjacent nucleation units in the fractals assemble in a straight line and form rods. Subsequently, the rods flatten out into rough and then into smooth ribbons. Occasionally, tubular membrane vesicles are formed from the fractals. The aggregation stage seems to be analogous to colloidal aggregation and amyloid fiber formation. The fusion stage seems to be characteristic of the lipid-rich lipoproteins and is beyond colloidal aggregation and amyloid fiber formation.     

The ‘president’s drug’

Netherlands Heart Journal -     

The cave bear’s hibernation: reconstructing the physiology and behaviour of an extinct animal

Abstract

When studying an extinct species such as the cave bear (Ursus spelaeus ROSENMÜLLER 1794), it is possible to apply a variety of molecular biology techniques such as the study of stable isotopes or mitochondrial DNA (mDNA) to infer patterns of behaviour or physiology that would otherwise remain concealed. Throughout Europe and along time, differences in the isotopic values (δ¹³C and δ¹⁵N) of cave bears arise from environmental differences and the Pleistocene climatic evolution. The climate determines the hibernation length, during which the cave bears undergo a particular physiology that can be related to an increase in δ¹⁵N during climate cooling. In order to verify whether hibernation affected the isotopic values, we compared cave bears in different ontogenetic stages. The results show that perinatal values reflect the values for mothers during hibernation, while juveniles show differences in maternal investment. A previous study in the literature based on complete mitochondrial DNA sequences of several individuals collected from closely situated caves showed that each cave housed, almost exclusively, a single lineage of haplotypes. This pattern suggests extreme fidelity to the birth site, or homing behaviour, and that cave bears formed stable maternal social groups, at least for the purpose of hibernation. Studies of this type offer unexpected data on the palaeobiology of this extinct animal.     

The Everglades: North America’s subtropical wetland

The Everglades is the largest subtropical wetland in the United States. Because of its size, floral and faunal diversity, geological history and hydrological functions on the Florida landscape, the remaining Everglades are considered to be the crown jewel of U.S. wetlands. It is also called a “sentinel wetland” to test our society’s resolve for ecosystem restoration. Originally called Pa-hay-okee (“grassy lake”) by the American Indians, it was later popularized as the “river of grass” by Marjory Stoneman Douglas. This metaphor unfortunately has led to a simplistic view of the complexities of the Everglades ecosystem and how it functions on the landscape. Often incorrectly referred to as the “marsh” or “swamp,” the Everglades is a fen peatland or alkaline mire. These are important distinctions when one considers how different marshes and swamps are from peatlands in terms of their hydrologic controls, biogeochemistry, rate of peat development, plant and animal communities and-importantly-succession patterns. This paper provides a brief review of the geological processes that led to the development of the Everglades, compares historic and current hydrologic flow patterns, assesses nutrient conditions, presents information on vegetation communities and succession patterns, and provides a new peatland classification of the Everglades system, which may help in the development of a more appropriate restoration management framework.     

NADPH oxidase: an enzyme for multicellularity?

Multicellularity has evolved several times during the evolution of eukaryotes. One evolutionary pressure that permits multicellularity relates to the division of work, where one group of cells functions as nutrient providers and the other in specialized roles such as defence or reproduction. This requires signalling systems to ensure harmonious development of multicellular structures. Here, we show that NADPH oxidases are specifically present in organisms that differentiate multicellular structures during their life cycle and are absent from unicellular life forms. The biochemical properties of these enzymes make them ideal candidates for a role in intercellular signalling.     

The UK’s 100,000 Genomes Project: manifesting policymakers’ expectations

The UK’s 100,000 Genomes Project has the aim of sequencing 100,000 genomes from UK National Health Service (NHS) patients while concomitantly transforming clinical care such that whole genome sequencing becomes routine clinical practice in the UK. Policymakers claim that the project will revolutionize NHS care. We wished to explore the 100,000 Genomes Project, and in particular, the extent to which policymaker claims have helped or hindered the work of those associated with Genomics England – the company established by the Department of Health to deliver the project. We interviewed 20 individuals linked to, or working for Genomics England. Interviewees had double-edged views about the context within which they were working. On the one hand, policymakers’ expectations attached to the venture were considered vacuous “genohype”; on the other hand, they were considered the impetus needed for those trying to advance genomic research into clinical practice. Findings should be considered for future genomes projects.     

The cashew’s brighter future

The cashew tree, native to Brazil was introduced into India in the 16th century for the purpose of checking erosion on the coasts. India is a world leader in the production and export of cashew nuts, while cultivation of this crop in the western hemisphere has remained negligible. Present demand far exceeds the supply. New developments in processing methods and machinery, and new uses for by-products, particularly cashew shell oil, have stimulated cashew culture in East Africa and Brazil and should give impetus to establishment of this lucrative crop on a commercial basis in other tropical areas.