Last judgment: the visionary biology of J.B.S. Haldane

This paper seeks to reinterpret the life and work of J. B. S. Haldane by focusing on an illuminating but largely ignored essay he published in1927, “The Last Judgment” – the sequel to his better known work, Daedalus (1924). This astonishing essay expresses a vision of the human future over the next 40,000,000 years, one that revises and updates Wellsian futurism with the long range implications of the “new biology” for human destiny. That vision served as a kind of lifelong credo, one that infused and informed his diverse scientific work, political activities, and popular writing, and that gave unity and coherence to his remarkable career. This revised version was published online in July 2006 with corrections to the Cover Date.     

The origins of human gene mapping. With particular reference to the contributions of J. B. S. Haldane

Methods in human gene mapping, including those developed by Bell and Haldane, Morton, and the more recent ones using somatic cell fusion, restriction fragment length polymorphism (RFLP), and multipoint linkage, are briefly reviewed.     

Digital microscopy in phycological research, with special reference to microalgae

Digital imaging technology is gradually being incorporated into all areas of biological research, but there is a distinct lack of information resources targeted at scientists in their specialist areas. There is a wealth of potential applications for digital images in phycology, including morphometric or visual analysis of specimens, taxonomic databases and publication of digital micrographs in lieu of photomicrographs. Here, we provide a review of digital imaging in general and its potential for the field of microalgal research in particular. We also present a number of imaging techniques that are critical for image acquisition and optimization, which can enable beginners to build their own libraries of high quality digital images. Resolution requirements of digital cameras are explained and related to microscope resolution. The benefits of digital imaging technology are discussed and contrasted with those of traditional silver halide technology.     

Development trends in taxonomy,with special reference to fungi

Taxonomy is a traditional subject, but it still receives attention and has become a topic of much discussion in recent years. Many of these discussions have raised concerns about the future of taxonomy, especially with regard to the workforce responsible for the discovery of new species in the context of declining biodiversity. Previous discussions were based on the taxonomic data of plants and animals, but the status of fungal taxonomy has not been mentioned. Fungi have one of the highest levels of biodiversity among all living organisms, second only to insects. The discussion of the future of taxonomy without the inclusion of fungal data is incomplete. Here, we present the results of analyses based on all new fungal taxa published since 1753. Fungal taxonomy is an ever‐growing area of study with increasing numbers of new taxa being described and growing numbers of fungal taxonomists. Compared with plants and most animal groups, there has been a much sharper increase in the rate at which new fungal taxa are being described. Furthermore, the number of taxonomists studying fungi has increased at a faster speed than those studying plants or animals. This indicates that fungal taxonomy is a prosperous subject and a dynamic area for scientific studies, and that it deserves much more attention and support. The study of fungal taxonomy will deepen our understanding of the biodiversity of our planet.     

Culture-independent analysis of fecal microbiota in infants, with special reference to Bifidobacterium species

Fecal microbiota of 31 breast-fed, 26 mix-fed, and 11 bottle-fed infants were analyzed by using terminal restriction fragment length polymorphism (T-RFLP), and culture method. We first determined the total and cultivated bacterial counts in infant fecal microbiota. Only approximately 30% of bacteria present in fecal microbiota were cultivable while the remainder was yet-to-be cultured bacteria. Sixty-eight fecal samples were divided into two clusters (I and II) by T-RFLP analysis, and then subdivided into five subclusters (Ia, Ib, IIa, IIb and IIc). There was no clear relationship between clusters and feeding method. A proportion of bifidobacteria was detected in the fecal material by PCR method using species-specific primers. The predominant Bifidobacterium spp. was Bifidobacterium longum longum type (43 samples (63.2%)), followed by B. longum infantis type (23 samples (33.8%)) and B. breve (16 samples (23.5%)). The distribution of Bifidobacterium spp. was similar in the three feeding groups. In contrast, the high incidence of B. breve in cluster I, especially subcluster Ia and B. longum longum type in cluster II, especially subcluster IIa and IIc were characterized by T-RFLP method. Our results showed that the colonization of Bifidobacterium spp. in infant feces correlated with the T-RFLP clusters.     

Haplotype variation in the ACE gene in global populations, with special reference to India, and an alternative model of evolution of haplotypes

Angiotensin-I-converting enzyme (ACE) is known to be associated with human cardiovascular and psychiatric pathophysiology. We have undertaken a global survey of the haplotypes in ACE gene to study diversity and to draw inferences on the nature of selective forces that may be operating on this gene. We have investigated the haplotype profiles reconstructed using polymorphisms in the regulatory (rs4277405, rs4459609, rs1800764, rs4292, rs4291), exonic (rs4309, rs4331, rs4343), and intronic (rs4340; Alu [I/D]) regions covering 17.8 kb of the ACE gene. We genotyped these polymorphisms in a large number of individuals drawn from 15 Indian ethnic groups and estimated haplotype frequencies. We compared the Indian data with available data from other global populations. Globally, five major haplotypes were observed. High-frequency haplotypes comprising mismatching alleles at the loci considered were seen in all populations. The three most frequent haplotypes among Africans were distinct from the major haplotypes of other world populations. We have studied the evolution of the two major haplotypes (TATATTGIA and CCCTCCADG), one of which contains an Alu insertion (I) and the other a deletion (D), seen most frequently among Caucasians (68%), non-African HapMap populations (65?C88%), and Indian populations (70?C95%) in detail. The two major haplotypes among Caucasians are reported to represent two distinct clades A and B. Earlier studies have postulated that a third clade C (represented by the haplotypes TACATCADG and TACATCADA) arose from an ancestral recombination event between A and B. We find that a more parsimonious explanation is that clades A and B have arisen by recombination between haplotypes belonging to clade C and a high-frequency African haplotype CCCTTCGIA. The haplotypes, which according to our hypothesis are the putative non-recombinants (PuNR), are uncommon in all non-African populations (frequency range 0?C12%). Conversely, the frequencies of the putative recombinant haplotypes (PuR) are very low in the Africans populations (2?C8%), indicating that the recombination event is likely to be ancient and arose before, perhaps shortly prior to, the global dispersal of modern humans. The global frequency spectrum of the PuR and the PuNR is difficult to explain only by drift. It appears likely that the ACE gene has been undergoing a combination of different selective pressures.     

mtDNA polymorphism in East Asian Populations,with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.     

Testis differentiation in the glowworm, Lampyris noctiluca, with special reference to the apical tissue.

The gonads of Lampyris noctiluca are sexually undifferentiated during the first larval instars. They consist of many gonadal follicles that include the germ stem cells enclosed by the somatic cells of the follicle wall. Follicle wall cells are more numerous at the follicle apices than at the distal parts, but different cell types cannot be distinguished. In male larvae, the appearance of apical follicle tissue, derived from follicle wall cells, marks the onset of testis differentiation. When maximally expressed, the apical tissue occupies about the upper half of the testis follicles and can be observed in larvae of the fifth and sixth instar. The apical tissue is characterized by its "light" appearance (due to poor stainability) caused by the small number cellular organelles, especially a paucity of free ribosomes. Maximal expression of the apical tissue must be very brief, since in most examined fifth and sixth instar larvae the apical tissue is partly or mostly translocated into the center of the upper half of the follicles and spermatogonia then occupy the apical follicle tips. During and after translocation apical cells form projections that grow around clusters of spermatogonia (spermatocysts). Thus, the apical cells transform into spermatocyst envelope cells. They retain their "light" appearance but undergo dramatic subcellular differentiation: smooth ER becomes extremely prominent, forming stacks and whorls of parallel cisternae. Golgi complexes are also conspicuous. The cellular organization suggests secretory activity. The possibility of ecdysteroid production and its function is discussed. The spermatocyst envelope cells persist into the pupal stage. When spermiohistogenesis takes place in cysts, cyst envelope cells show signs of regression. At all stages of testis development apical cells and their derivatives, the spermatocyst envelope cells, phagocytize degenerating spermatogonia. Although this is an important task of these cells, the impressive formation of sER in the cyst envelope cells is indicative of an additional, as yet unknown, function.     

Physico-chemical environment in Tjeukemeer with special reference to speciation of algal nutrients

This paper attempts to generalize the major controlling factors and their impacts on the physico-chemical environment in Tjeukemeer in relation to the speciation of algal nutrients.Morphometry, man-made hydrology, climate, chemistry of drainage area and biology of the lake appear to control its physico-chemistry the most. Thus the shallow Tieukemeer is vulnerable to wind and therefore almost always completely mixed and often turbid owing to resuspended sediments. In normal summers the lake is oligohaline, hard, eutrophic and alkaline, and in winter it is hard, eutrophic, alkaline and humus-rich. The implications of these properties on the following physico-chemical components and their relevance for the speciation of algal nutrients are discussed: turbidity, colour, halinity, pH, alkalinity, salinity, conductivity, ionic composition, ionic balance and organic matter.Because of the relationships between the physico-chemical environment on the one hand and the speciation and bio-availability of nutrients on the other hand, special attention is given to the speciation of some major and minor elements as derived from ultra filtration experiments. In this context, the metal binding capacity of the organic matter (mainly fulvic acids) is also considered.     

Genetics of the butterfly Danaus chrysippus (L.) in a broad hybrid zone, with special reference to sex ratio, polymorphism and intragenomic conflict

The aposematic savanna butterfly Danaus chrysippus seems to be an exception to the rule that Batesian models and Müllerian mimics are not polymorphic. Throughout Asia and in much of Africa the species is in fact monomorphic and polytypic, as expected. It is, however, polymorphic for 3–4 colour genes over a large area of central and eastern Africa, where deviant sex ratios and non-Mendelian segregations also occur. All-female broods are widespread and frequent, often outnumbering bisexual progenies and giving rise to heavily female-biased populations. Full and partial sex linkage, which is not controlled from the X or Y chromosomes, and male-biased broods also occur. Genetical analysis for the BC-autosome carrying colour genes suggests there are two, probably mitochondrial, cytotypes (microbe-induced early male death syndrome is considered unlikely) and an autosomal, incompatibility (I) gene, two alleles of which are male-specific killers. F2 and backcross matings by females heterozygous at the 1-locus give progenies which are either thelygenic, all males dying at or soon after hatching, or bisexual but showing full or partial sex linkage. Male death is attributed to nuclear-cytoplasmic incompatibility (NCI). Females achieve reversion from a thelygenic to a bisexual line by mating with males of compatible (maternal) cytotype. A second NCI system causes meiotic drive in female oögenesis for a cytoplasmically compatible A-autosome, with no effect on SR. The array of non-Mendelian segregations for sex and two autosomes, with switching between bisexual and unisexual lineages, indicates autosomal intragenomic conflict with the outcome that one autosome is preserved from elimination in females and the other condemned in dead males. The geographical distribution of the colour marker genes suggests that the polymorphisms have a hybrid origin involving several once allopatric subspecies, some of which have divergent cytotypes. Secondary contact probably followed range expansion induced by the periodic spread of savanna during the Pleistocene and massive deforestation by man in recent times. The unusual extent of the hybrid zone is attributed to the large number of subspecies involved in its origin, and to introgression promoted by the butterfly's extensive migratory activity.     

18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea,Euglenozoa) with special reference to Trypanosoma

Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions that require robust phylogenetic markers to increase the resolution of trees. Using two known 18S rRNA gene template structures (from Trypanosoma cruzi Chagas, 1909 and Trypanosoma brucei Plimmer and Bradford, 1899), individual 18S rRNA gene secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood. The reconstructed trees allowed us to discuss not only the big picture of trypanosomatid phylogeny but also a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity. The robust support (bootstrap > 75) for well-known clades and critical branches suggests that the simultaneous use of 18S rRNA sequence and secondary structure data can reconstruct robust phylogenetic trees and can be used by the trypanosomatid research community for future analysis.     

Differences in surface-dwelling beetles of grasslands invaded and non-invaded by goldenrods (Solidago canadensis,S. gigantea) with special reference to Carabidae

We evaluated surface-dwelling Coleoptera with special reference to ground beetles (Coleoptera: Carabidae) using pitfall traps across fourteen stands of grasslands invaded and non-invaded by invasive goldenrods (Solidago canadensis L. and S. gigantea Ait.) over a 3 year period. We analysed differences in assemblages of invaded and non-invaded grasslands and tested responses of surface-dwelling beetles and carabids to invasion of goldenrods. We identified 29 Coleoptera families and 91 Carabidae species. Solidago invaded grasslands showed significantly higher activity-abundance of rove and carrion beetles and supported greater diversity and significantly higher evenness of surface-dwelling Coleoptera and the number of sampled families and individuals was higher too. We found lower taxonomic richness and significantly lower activity-abundance of carabids across goldenrods stands. Several less common Carabidae species and significantly higher representation of stenotopic brachypterous habitat specialists were also observed within invaded stands. We confirmed that differences in plant cover connected with invasion of goldenrods, soil moisture and abandonment of invaded habitats are the driving mechanisms of changes in surface-dwelling Coleoptera and ground beetles assemblages composition across Solidago invaded grasslands. Overall, changes of grassland biotopes connected with invasion of goldenrods significantly alter Coleoptera families and Carabidae assemblages, but not necessarily reduce diversity.