Compensatory nature of Chargaff’s second parity rule

The second parity rule of Chargaff (A≈T and G≈C within one strand) holds all over the living world with minor exceptions. It is maintained with higher accuracy for long sequences. The question addressed in the article is how different sequence types, with different biases from the parity, contribute to the general effect. It appears that the sequence segments with biases of opposite sign are intermingled, so that with sufficient sequence lengths the parity is established. The parity rule seems to be a cumulative result of a number of independent processes in the genome evolution, with the parity as their intrinsic property. Symmetrical appearance of simple repeats and of Alu sequences in the human DNA strands, and other contributions to the Chargaff parity II rule are discussed.     

Trinucleotide’s quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff’s second parity rule

For almost 50 years the conclusive explanation of Chargaff’s second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson–Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson–Crick base pairing generates CSPR. We demonstrate quadruplet’s symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These “landscapes” are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1–12, and X, Y the “landscapes” are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.     

Acid-mediated Lipinski’s second rule: application to drug design and targeting in cancer

With a predicted 382.4 per 100,000 people expected to suffer from some form of malignant neoplasm by 2015, and a current death toll of 1 out of 8 deaths worldwide, improving treatment and/or drug design is an essential focus of cancer research. Multi-drug resistance is the leading cause of chemotherapeutic failure, and delivery of anticancer drugs to the inside of cancerous cells is another major challenge. Fifteen years ago, in a completely different field in which improving drug delivery is the objective, the bioavailability of oral compounds, Christopher Lipinski formulated some rules that are still used by the pharmaceutical industry as rules of thumb to improve drug delivery to their target. Although Lipinski’s rules were not formulated to improve delivery of antineoplastic drugs to the inside of cancer cells, it is interesting to note that the problems are similar. On the basis of the strong similarity between the fields, we discuss how they can be connected and how new drug targets can be defined in cancer.     

Sociology is an applied science,and the application is social change: a contribution to the discussion of Aldon Morris’ The Scholar Denied

I argue that W.E.B. Du Bois’ expulsion from academic sociology at the beginning of the twentieth century was not only animated by the gatekeepers’ desire to maintain academe as a whites-only domain. It also constituted an active effort to defend Social Darwinist dogma, which dominated (white) social science at that time, from the formidable challenge of a resourceful and scientifically superior perspective. The successful exclusion of Du Bois (and his growing legion of colleagues) allowed sociology to drift into functionalist dogma, with its immutable hierarchy and denial of sociology’s role in facilitating social change. The exclusion of Du Boisean analysis, which placed human agency – and especially subaltern groups – at the centre of social change – rendered sociological analysis irrelevant to addressing social problems and social justice, until the Civil Rights Movement in America broke down the walls of the sociological ghetto, allowing it to access the rich Du Boisean perspective.     

Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70th birthday

This issue of Biophysical Reviews, titled ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, is a collection of articles dedicated in honour of Professor Fumio Arisaka’s 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.     

Balancing costs and confidence: volunteer-provided point observations,GPS telemetry and the genetic monitoring of Finland’s wolves

Reliable and updated population estimates are a necessity for the successful conservation and management of endangered animal populations. Citizen science has become increasingly important in wildlife monitoring and is an attractive concept due to its low costs. However, the applicability of citizen science in the monitoring of large carnivore populations is questionable for various reasons, including the difficulties associated with species identification. In Finland, where estimates of the fragmentary wolf (Canis lupus) population have varied between 140 and 280 animals in the last 10 years, population monitoring has been based on volunteer-provided data and telemetry. To compensate for a recent decrease in the proportion of territories with boundaries mapped through telemetry, a non-invasive genetics project was launched in 2016. We evaluated the experiences from this project, in which non-invasive genetic techniques were, for the first time, widely used (n?=?22 territories, 54% of the 41 apparent territories hosted by wolves in March 2017) to determine the post-hunting population estimate in early March 2017, before pack sizes began to decrease due to dispersal by sub-adult wolves. In territories where the non-invasive genetic monitoring was executed in the winter of 2016/2017, the pack sizes resulting from the volunteer-provided observations and the genetic analyses were highly correlated. By using the most typical variation in the proportion of non-residents in the wolf populations (6–20%, Fuller et al. 2003), we derived a population estimate of 150–178 wolves for early March 2016, and, by considering the known mortality during the study period, a minimum estimate of 204–234 wolves for early Aug. 2016. Despite its high costs, we recommend that non-invasive genetic monitoring should cover all known territories supporting Finland’s small and exploited wolf population. This much costlier protocol may be unrealistic in Finland. In any case, there is a need for more genetic sampling to test the quality of volunteer-provided data.     

Coming to America: Acclimation in macaque body structures and Bergmann’s rule

I analyzed somatometric measurements from subsets of the Texas and Oregon transplanted troops of Japanese macaques(Macaca fuscata) to reveal secular changes in body size and shape. Body weights of the Texas population (N = 59) are lower than those of the Oregon population(N = 49) and the founding population from Arashiyama. The adult weights of the Oregon population are significantly higher than the founding population from Mihara. There are significant differences in adult circumferential measures and in skinfolds, which are correlated with the increased weight of the Oregon macaques. The adult Texas macaques have longer limb segments in comparison with the adult Oregon troop members, while the latter have significantly longer heads and trunks. Examination of the developing morphological trends through regression analyses on the complete sample suggests distinctive growth patterns for each population. Members of the Texas population start with smaller initial measurements but hold a steeper growth pattern for limb segments, while the Oregon macaques start larger in most measures and show lower growth rates. I argue that these differences in both somatometry and growth patterns are related to the differing climatic conditions under which the translocated macaques have lived. This set of analyses supports the basic arguments for Bergmann’s rule and Allen’s rule.     

Protein complex finding and ranking: An application to Alzheimer’s disease

Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein–protein interactions (PPIs) is an important area of research. Earlier work has been limited mostly to yeast and a few other model organisms. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called ComFiR to detect such protein complexes and further rank diseased complexes based on a query disease. We have shown that it has better performance in identifying protein complexes from human PPI data. This method is evaluated in terms of positive predictive value, sensitivity and accuracy. We have introduced a ranking approach and showed its application on Alzheimer’s disease.     

Biomechanism of impact resistance in the woodpecker’s head and its application

The woodpecker does not suffer head/eye impact injuries while drumming on a tree trunk with high acceleration(more than 1000×g) and high frequency.The mechanism that protects the woodpecker’s head has aroused the interest of ornithologists,biologists and scientists in the areas of mechanical engineering,material science and electronics engineering.This article reviews the literature on the biomechanisms and materials responsible for protecting the woodpecker from head impact injury and their applications in engineering and human protection.     

One hundred years of continental drift: the early Italian reaction to Wegener’s ‘visionary’ theory

One hundred years ago in 1915 ‘Die Entstehung der Kontinente und Ozeane’ by Alfred Wegener was published, destined to become one of the most controversial geological opus in the first half of the twentieth century. Wegener is the first to combine the most diverse geological (sensu lato) evidences in a single great synthesis. Nonetheless, apart from few upholders, the initial reaction to the drift hypothesis was fierce opposition, and the strongest criticism came from geophysics, the same discipline that, paradoxically, starting from the 1950s led to the Plate Tectonics revolution and, ultimately, to a complete re-evaluation of Wegener’s hypothesis. In the present paper we discuss the initial reaction of Italian scientists to the original continental drift theory, with particular focus on the period between the two world wars. Italian geologists like Fossa-Mancini and Gortani were almost favourable to the new theory, while authors such as Vardabasso and Sacco were neutral or even hostile to the new hypothesis, so iconoclastic for the widely accepted fixist vision of the time. In any case, all these scientists agreed that the new theory had great potential for reopening an enthusiastic debate on issues that were given as established paradigms – the genuine way for progress in science.     

Scaling of species diversity and body mass in mammals: Cope’s rule and the evolutionary cost of large size

Abstract

Equations are constructed describing the inverse correlation of species diversity and body mass in extant and Cenozoic mammals. Cope’s rule, the tendency for many mammal clades to increase in body size through time, through phyletic change in single lineages or turnover within species groups, is interpreted as a probability function reducing diversity potential as a tradeoff for ecological/evolutionary gains. The inverse rule predicts that large species in clades will be less diverse than smaller species and, unless origination rates remain high among smaller clade members, clades conforming to Cope’s rule will decline in diversity, moving towards extinction. This proposition is evaluated in the Cenozoic histories of five North American mammal clades; cotton rats, felids, canids, hyaenodontids, and equids. Diversity potential of different size classes within the 3.75 million year phyletic history of the muskrat, Ondatra zibethicus, is also examined. A corollary prediction of the inverse rule, that large species should have longer durations (species lifespans) than small species, is unresolved. Successful clades maintain small size or a significant number of smaller species relative to clade average size. The potential loss of unique extant large mammal species justifies the conservation effort to protect them. The similarity of scaling exponents of species diversity to mass around a slope of -1.0 suggests that species diversity is correlated with home range size, the latter related to the probability of population fragmentation.     

Plant individuality: a solution to the demographer’s dilemma

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800; Braun and Stone 1853; Münch 1938) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977; Cook 1985; Ariew and Lewontin 2004), a lively debate conducted mostly in Scandinavian journals proves that the issues are far from being resolved (Tuomi and Vuorisalo 1989b; Fagerström 1992; Pan and Price 2001). In this paper I settle the matter once and for all, by showing which elements of each side are correct.     

A case of Kartagener’s syndrome: Importance of early diagnosis and treatment

Kartagener’s syndrome is a very rare congenital malformation comprising of a classic triad of sinusitis, situs inversus and bronchiectasis. Primary ciliary dyskinesia is a genetic disorder with manifestations present from early life and this distinguishes it from acquired mucociliary disorders. Approximately one half of patients with primary ciliary dyskinesia have situs inversus and, thus are having Kartagener syndrome. We present a case of 12 year old boy with sinusitis, situs inversus and bronchiectasis. The correct diagnosis of this rare congenital autosomal recessive disorder in early life is important in the overall prognosis of the syndrome, as many of the complications can be prevented if timely management is instituted, as was done in this in this case.