Extra-Mediterranean refugia: The rule and not the exception?

ABSTRACT: Some decades ago, biogeographers distinguished three major faunal types of high importance for Europe: (i) Mediterranean elements with exclusive glacial survival in the Mediterranean refugia, (ii) Siberian elements with glacial refugia in the eastern Palearctic and only postglacial expansion to Europe and (iii) arctic and/or alpine elements with large zonal distributions in the periglacial areas and postglacial retreat to the North and/or into the high mountain systems. Genetic analyses have unravelled numerous additional refugia both of continental and Mediterranean species, thus strongly modifying the biogeographical view of Europe. This modified notion is particularly true for the so-called Siberian species, which in many cases have not immigrated into Europe during the postglacial period, but most likely have survived the last, or even several glacial phases, in extra-Mediterranean refugia in some climatically favourable but geographically limited areas of southern Central and Eastern Europe. Recently, genetic analyses revealed that typical Mediterranean species have also survived the Last Glacial Maximum in cryptic northern refugia (e.g. in the Carpathians or even north of the Alps) in addition to their Mediterranean refuge areas.     

The origin of life and the left-handed amino-acid excess: the furthest heavens and the deepest seas?

The origin of life is an extraordinary problem that leads back to the structure and dynamics of the cosmos and early development of organic molecules. Within that wider question lies an unsolved problem that has troubled biologists for 150 years. What is the origin of the dominant presence of left-handed stereoisomers of amino acids in nature even though their synthesis normally results in an equal mixture of the right- and left-handed molecular forms? We propose that asymmetric Earth rotation caused at dawn and dusk circularly polarized UV light (CPUVL) of opposite polarity and reversed temperature profiles in the oceans. Destruction of the d-isomer by CPUVL at dusk in a sea surface hotter than at dawn created a daily l-isomer excess protected from radiation by nightfall, preserved by down-flow (diffusive, mechanical) into cold, darker regions, eventually initiating an l-amino-acid excess embodied in early marine forms. Innumerable mechanisms have been proposed for the origin of l-chiral dominance in amino acids and none proven. Since the thalidomide tragedy, homochirality of amino acids has been a growing practical issue for medicine. Understanding its origin may bring further and unexpected benefits. It may also be a modest pointer to the possibility of positive answers to whether intelligent life will have the capacity to continue to protect itself from conditions inimical to survival.     

The pen and the sword: recovering the disciplinary identity of physiology and anatomy before 1800: II: Old anatomy—the sword

Following the exploration of the disciplinary identity of physiology before 1800 in the previous paper of this pair, the present paper seeks to recover the complementary identity of the discipline of anatomy before 1800. The manual, artisanal character of anatomy is explored via some of its practitioners, with special attention being given to William Harvey and Albrecht von Haller. Attention is particularly drawn to the important role of experiment in anatomical research and practice—which has been misread by historians as physiological experiment. Although scientific status was claimed by some practitioners for the discipline, the knife remained the tool of the discipline. Finally the differences between the teleological assumptions underlying anatomy, and the ‘argument from design’ or natural theology are explored.     

The thymus and T-cell commitment: the right niche for Notch?

The current dogma is that the thymus is colonized by progenitors that retain the capacity to generate both T cells and B cells, and that intrathymic Notch signalling determines lineage choice so that T cells, rather than B cells, develop in the thymus. However, evidence is now accumulating to indicate that, at least during fetal life, this is not the case. Rather, it now seems that the fetal thymus is colonized by progenitors that have already made the T-cell versus B-cell lineage choice. We propose an alternative role for Notch signalling in the thymus, which is not to mediate this choice but instead to reveal it by supporting further T-cell differentiation in the thymic microenvironment.     

The “Island Rule” and Deep-Sea Gastropods: Re-Examining the Evidence

Background

One of the most intriguing patterns in mammalian biogeography is the “island rule”, which states that colonising species have a tendency to converge in body size, with larger species evolving decreased sizes and smaller species increased sizes. It has recently been suggested that an analogous pattern holds for the colonisation of the deep-sea benthos by marine Gastropoda. In particular, a pioneering study showed that gastropods from the Western Atlantic showed the same graded trend from dwarfism to gigantism that is evident in island endemic mammals. However, subsequent to the publication of the gastropod study, the standard tests of the island rule have been shown to yield false positives at a very high rate, leaving the result open to doubt.

Methodology/Principal Findings

The evolution of gastropod body size in the deep sea is reexamined. Using an extended and updated data set, and improved statistical methods, it is shown that some results of the previous study may have been artifactual, but that its central conclusion is robust. It is further shown that the effect is not restricted to a single gastropod clade, that its strength increases markedly with depth, but that it applies even in the mesopelagic zone.

Conclusions/Significance

The replication of the island rule in a distant taxonomic group and a partially analogous ecological situation could help to uncover the causes of the patterns observed—which are currently much disputed. The gastropod pattern is evident at intermediate depths, and so cannot be attributed to the unique features of abyssal ecology.     

Linkage in the mouse: The sex-linked genes and “rough”

Molecular Genetics and Genomics - The order of the totally sex-linked genes and the recombination frequencies in heterozygous females are — $$B_n - 11\% - Ta - 4\% - \left\{ {_{Mo}^{Br} }...     

DNA polymerase ι: The long and the short of it!

The cDNA encoding human DNA polymerase ι (POLI) was cloned in 1999. At that time, it was believed that the POLI gene encoded a protein of 715 amino acids. Advances in DNA sequencing technologies led to the realization that there is an upstream, in-frame initiation codon that would encode a DNA polymerase ι (polι) protein of 740 amino acids. The extra 25 amino acid region is rich in acidic residues (11/25) and is reasonably conserved in eukaryotes ranging from fish to humans. As a consequence, the curated Reference Sequence (RefSeq) database identified polι as a 740 amino acid protein. However, the existence of the 740 amino acid polι has never been shown experimentally. Using highly specific antibodies to the 25 N-terminal amino acids of polι, we were unable to detect the longer 740 amino acid (ι-long) isoform in western blots. However, trace amounts of the ι-long isoform were detected after enrichment by immunoprecipitation. One might argue that the longer isoform may have a distinct biological function, if it exhibits significant differences in its enzymatic properties from the shorter, well-characterized 715 amino acid polι. We therefore purified and characterized recombinant full-length (740 amino acid) polι-long and compared it to full-length (715 amino acid) polι-short in vitro. The metal ion requirements for optimal catalytic activity differ slightly between ι-long and ι-short, but under optimal conditions, both isoforms exhibit indistinguishable enzymatic properties in vitro. We also report that like ι-short, the ι-long isoform can be monoubiquitinated and polyubiuquitinated in vivo, as well as form damage induced foci in vivo. We conclude that the predominant isoform of DNA polι in human cells is the shorter 715 amino acid protein and that if, or when, expressed, the longer 740 amino acid isoform has identical properties to the considerably more abundant shorter isoform.     

The worm and the protozoa: stereotyped responses or distinct antigens?

Studies of parasitic diseases have provided the best in vivo correlates of the division of CD4+ helper T cells into distinct functional phenotypes, designated T(H)I and T(H)2, that mediate the balanced regulation of cellular and humoral immunity. In this article, Steven Reiner and Richard Locksley focus on why parasitic infections tend to generate such clearly polarized responses and emphasize that early events that mediate maturation signals towards T(H)1- or T(H)2-effector and memory cells remain incompletely defined. Effective vaccination that seeks to mold the developing immune response will need to consider the role of interleukins and various cell-surface molecules that have been identified, thus far, to influence CD4 subset differentiation.