Amazing structure of respirasome: unveiling the secrets of cell respiration

Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang’s group from Tsinghua University (Gu et al.Nature 237(7622):639–643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening. However, the study of cellular respiration went through a long history. Here, we briefly showed the detoured history of respiratory chain investigation, and then described the amazing structure of respirasome.     

Ancient DNA Reveals Matrilineal Continuity in Present-Day Poland over the Last Two Millennia

While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC – 500 AD (Roman Iron Age) and for 20 samples dated to 1000–1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age.     

The trade-off between a high and an equal biological standard of living—Evidence from Germany

Following German re-unification, East Germany moved from a state-socialist to a market-based economic system. Using West Germany as a “control group”, we examine how the change affected the level and the equality of the biological standard of living. We find that before unification, East Germany had a lower but somewhat more equally distributed biological standard of living than the West. After unification, East Germany rapidly caught up in terms of height but at the expense of equality. This suggests that a trade-off exists between a high and an equally distributed biological standard of living. Unlike previous research, we find that West Germany's pre-unification height advantage was smallest in towns with 5000-20,000 inhabitants and largest in cities with 20,000-100,000 inhabitants (females) or in cities with more than 100,000 inhabitants (males). Between regions, height converged both in East and West Germany, but particularly markedly among East-German males. Equality convergence, like height convergence, is significantly larger for East than for West-German males.     

Health of infants in an Imperial Roman skeletal sample: perspective from dental microstructure

This study examines general health in the first year of life of a population of 127 subadults from the Imperial Roman necropolis of Isola Sacra (2nd-3rd century ACE). Health status was determined by analyzing 274 deciduous teeth from these children for Wilson bands (also known as accentuated striae), microscopic defects caused by a disruption to normal enamel development arising from some generalized external stressor. While macroscopic enamel defects, or hypoplasias, have long been used as proxies of general population health, we believe that this is the first population-wide study of microscopic defects in deciduous teeth. We used microstructural markers of enamel to attach very precise chronologies to Wilson band formation that allowed us to calculate maximum prevalence (MAP) and smoothed maximum prevalence (SMAP) distributions to portray what we believe to be a realistic risk profile for a past population of children. There appear to be two periods of high prevalence, the first beginning around age 2 months and continuing through month 5, and the second higher period beginning around month 6 and continuing through month 9. These results are discussed in light of historical records of Roman childhood rearing practices.     

Evolution of human growth

The human pattern of growth and development (ontogeny) appears to differ markedly from patterns of ontogeny in other primate species. Humans present complex and sinuous growth curves for both body mass and stature. Many human proportions change dramatically during ontogeny, as we reach sizes that are among the largest of living primates. Perhaps most obviously, humans grow for a long time, with the interval between birth and maturation exceeding that of all other primate species. These ontogenetic traits are as distinctive as other key derived human traits, such as a large brain and language. Ontogenetic adaptations are also linked to human social organization, particularly by necessitating high levels of parental investment during the first several years of life.     

The effect of biota on global climate

A model consisting of two blocks (equations) was proposed for the analytical study of the biosphere-climate system over great periods of time. The first equation describes the balance of carbon dioxide in the atmosphere and represents the biological block of the model. The second equation is the equation of the energy balance or the physical block of the system. The model is based on the most general conceptions of living matter and the evolution process. A possible interpretation of some events and phenomena in the earth history in terms of the model is given.     

Human impact as registered in the pollen record: some results from the western Lake Constance region,Southern Germany

Pollen analytical results from a littoral profile taken in Lake Constance compared with pollen profiles from small kettle holes nearby form the basis for conclusions concerning human population density, the economy and environment from the Neolithic period to the Middle Ages. Early Neolithic human impact is implicated in a lime decline and also the expansion of beech. The late Neolithic lakeshore settlements caused a decline of elm, beech and lime and, by shifting cultivation, considerably changed the forest cover. The settlements were abandoned after less than 100 years. There were long periods without distinct human impact in the middle and towards the end of the late Neolithic period. Since at least the Late Bronze Age there has been permanent habitation in the region. Human impact was greatest in the High Medieval period and later, and was also substantial in the late La Tène and Roman periods. Distinct declines in human impact can be observed between the La Tène and Roman periods and in the Migration and Merovingian periods. In these intervals, open land and grazed oak forest were replaced by birch and later on by beech forests. The decreases in human impact are not of the same intensity in all diagrams.     

A cryptic taxon of Galápagos tortoise in conservation peril

As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.     

Patterns and drivers of intraspecific variation in avian life history along elevational gradients: a meta‐analysis

Elevational gradients provide powerful natural systems for testing hypotheses regarding the role of environmental variation in the evolution of life‐history strategies. Case studies have revealed shifts towards slower life histories in organisms living at high elevations yet no synthetic analyses exist of elevational variation in life‐history traits for major vertebrate clades. We examined (i) how life‐history traits change with elevation in paired populations of bird species worldwide, and (ii) which biotic and abiotic factors drive elevational shifts in life history. Using three analytical methods, we found that fecundity declined at higher elevations due to smaller clutches and fewer reproductive attempts per year. By contrast, elevational differences in traits associated with parental investment or survival varied among studies. High‐elevation populations had shorter and later breeding seasons, but longer developmental periods implying that temporal constraints contribute to reduced fecundity. Analyses of clutch size data, the trait for which we had the largest number of population comparisons, indicated no evidence that phylogenetic history constrained species‐level plasticity in trait variation associated with elevational gradients. The magnitude of elevational shifts in life‐history traits were largely unrelated to geographic (altitude, latitude), intrinsic (body mass, migratory status), or habitat covariates. Meta‐population structure, methodological issues associated with estimating survival, or processes shaping range boundaries could potentially explain the nature of elevational shifts in life‐history traits evident in this data set. We identify a new risk factor for montane populations in changing climates: low fecundity will result in lower reproductive potential to recover from perturbations, especially as fewer than half of the species experienced higher survival at higher elevations.     

The evolution of diversity in ancient ecosystems: a review

On a perfect planet, such as might be acceptable to a physicist, one might predict that from its origin the diversity of life would grow exponentially until the carrying capacity, however defined, was reached. The fossil record of the Earth, however, tells a very different story. One of the most striking aspects of this record is the apparent evolutionary longueur, marked by the Precambrian record of prokaryotes and primitive eukaryotes, although our estimates of microbial diversity may be seriously incomplete. Subsequently there were various dramatic increases in diversity, including the Cambrian ''explosion'' and the radiation of Palaeozoic-style faunas in the Ordovician. The causes of these events are far from resolved. It has also long been appreciated that the history of diversity has been punctuated by important extinctions. The subtleties and nuances of extinction as well as the survival of particular clades have to date, however, received rather too little attention, and there is still a tendency towards blanket assertions rather than a dissection of these extraordinary events. In addition, some but perhaps not all mass extinctions are characterized by long lag-times of recovery, which may reflect the slowing waning of extrinsic forcing factors or alternatively the incoherence associated with biological reassembly of stable ecosystems. The intervening periods between the identified mass extinctions may be less stable and benign than popularly thought, and in particular the frequency of extraterrestrial impacts leads to predictions of recurrent disturbance on timescales significantly shorter than the intervals separating the largest extinction events. Even at times of quietude it is far from clear whether biological communities enjoy stability and interlocked stasis or are dynamically reconstituted at regular intervals. Finally, can we yet rely on the present depictions of the rise and falls in the levels of ancient diversity? Existing data is almost entirely based on Linnean taxa, and the application of phylogenetic systematics to this problem is still in its infancy. Not only that, but even more intriguingly the pronounced divergence in estimates of origination times of groups as diverse as angiosperms, diatoms and mammals in terms of the fossil record as against molecular data point to the possibilities of protracted intervals of geological time with a cryptic diversity. If this is correct, and there are alternative explanations, then some of the mystery of adaptive radiations may be dispelled, in as much as the assembly of key features in the stem groups could be placed in a gradualistic framework of local adaptive response punctuated by intervals of opportunity.     

Fast x-ray fluorescence microtomography of hydrated biological samples

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples.     

Long life cycles in insects

Long life cycles covering more than one year are known for all orders of insects. There are different mechanisms of prolongation of the life cycle: (1) slow larval development; (2) prolongation of the adult stage with several reproduction periods; (3) prolongation of diapause; (4) combination of these mechanisms in one life cycle. Lasting suboptimal conditions (such as low temperature, low quality of food or instability of food resources, natural enemies, etc.) tend to prolong life cycles of all individuals in a population. In this case, the larvae feed and develop for longer than a year, and the active periods are interrupted by dormancy periods. The nature of this dormancy is unknown: in some cases it appears to be simple quiescence, in others it has been experimentally shown to be a true diapause. Induction and termination of these repeated dormancy states are controlled by different environmental cues, the day-length being the principal one as in the case of the annual diapause. The long life cycles resulting from prolonged adult lifespan were experimentally studied mainly in beetles and true bugs. The possibility of repeated diapause and several periods of reproductive activity is related to the fact that the adults remain sensitive to day length, which is the main environmental cue controlling their alternative physiological states (reproduction vs. diapause). Habitats with unpredictable environmental changes stimulate some individuals in a population to extend their life cycles by prolonged diapause. The properties of this diapause are poorly understood, but results of studies of a few species suggest that this physiological state differs from the true annual diapause in deeper suppression of metabolism. Induction and intensity of prolonged diapause in some species appear to be genetically controlled, so that the duration of prolonged diapause varies among individuals in a group, even that of sibles reared under identical conditions. Thus, long life cycles are realized due to the ability of insects to interrupt activity repeatedly and enter dormancy. This provides high resistance to various environmental factors. Regardless of the nature of this dormancy (quiescence, annual or prolonged diapause, or other forms) and the life cycle duration, the adults always appear synchronously after dormancy in the nature. The only feasible explanation of this is the presence of a special synchronizing mechanism, most likely both exo- and endogenous, since the adults appear not only synchronously but also in the period best suited for reproduction. As a whole, the long life cycles resulting from various structural modifications of the annual life cycle, are typical of the species living under stable suboptimal conditions when the pressure of individual environmental factors is close to the tolerance limits of the species, even though it represents its norm of existence. Such life cycles are also typical of the insects living in unstable environments with unpredictable variability of conditions, those developing in cones and galls, feeding on flowers, seeds, or fruits with limited periods of availability, those associated with the plant species with irregular patterns of blossoming and fruiting, and those consuming low-quality food or depending on unpredictable food sources (e.g., predators or parasites). Long cycles are more common in: (1) insect species at high latitudes and mountain landscapes where the vegetation season is short and unstable; (2) species living in deserts or arid areas where precipitation is unstable and often insufficient for survival of food plants; (3) inhabitants of cold and temporary water bodies that are not filled with water every year. At the same time, long life cycles sometimes occur in insects from other climatic zones as well. It is also important to note that while there is a large body of literature dealing with the long life cycles in insects, it mostly focuses on external aspects of the phenomenon. Experimental studies are needed to understand this phenomenon, first of all the nature of dormancy and mechanisms of synchronization of adult emergence.     

Stable isotope evidence for 1500 years of human diet at the city of York, UK

We present here the results of a large-scale diachronic palaeodietary (carbon and nitrogen isotopic measurements of bone collagen) study of humans and animals from a single site, the city of York (U.K.), dating from the Roman period to the early 19th century. The human sample comprises 313 burials from the cemeteries of Trentholme Drive and Blossom Street (Roman), Belle Vue House (Anglo-Saxon), Fishergate (High and Later Medieval), and All Saints, Pavement (Later and Post-Medieval). In addition, 145 samples of mammal, fish and bird bone from the sites of Tanner Row and Fishergate were analyzed. The isotope data suggest dietary variation between all archaeological periods, although the most significant change was the introduction of significant quantities of marine foods in the Medieval periods. These are first evident in the diet of a small group of individuals from the High Medieval cemetery at Fishergate, although they were consumed almost universally in the following periods. The human isotope values are also remarkable due to unusually elevated delta(15)N ratios that are not sufficiently explained by the comparably small enrichment in (13)C that accompanies them. We discuss the possible reasons behind this and the archaeological significance of the data set.     

Study of Harris lines at the Prat de la Riba necropolis--third to fifth century AD

Harris lines (HL) are considered a nutritional or pathological stress factor in the study of past populations. This study attempts to contribute to the knowledge of the causal agents for HL in terms of assessing the health state of the population of Tarragona in the Roman period. The presence of HL has been analyzed in 614 long bones (214 humeri, 150 femurs and 250 tibias) from 243 skeletons. No HL have been observed in humeri. The frequencies of HL in femurs are higher than 27% and in tibias more than 48%. Although no significant differences in the presence of HL is found among age categories, it seems that the causal agents of these marks acted on individuals from the age of 5, an age from which the long bones of the lower extremities are more prone to producing HL. The hardened living conditions in the Dark Age of the Roman period in Spain between the third to fifth centuries A.D. may be the cause of the high prevalence of HL in this population.     

Stature in archeological samples from central Italy: methodological issues and diachronic changes

Stature reconstructions from skeletal remains are usually obtained through regression equations based on the relationship between height and limb bone length. Different equations have been employed to reconstruct stature in skeletal samples, but this is the first study to provide a systematic analysis of the reliability of the different methods for Italian historical samples. Aims of this article are: 1) to analyze the reliability of different regression methods to estimate stature for populations living in Central Italy from the Iron Age to Medieval times; 2) to search for trends in stature over this time period by applying the most reliable regression method. Long bone measurements were collected from 1,021 individuals (560 males, 461 females), from 66 archeological sites for males and 54 for females. Three time periods were identified: Iron Age, Roman period, and Medieval period. To determine the most appropriate equation to reconstruct stature the Delta parameter of Gini (Memorie di metodologia statistica. Milano: Giuffre A. 1939), in which stature estimates derived from different limb bones are compared, was employed. The equations proposed by Pearson (Philos Trans R Soc London 192 (1899) 169-244) and Trotter and Gleser for Afro-Americans (Am J Phys Anthropol 10 (1952) 463-514; Am J Phys Anthropol 47 (1977) 355-356) provided the most consistent estimates when applied to our sample. We then used the equation by Pearson for further analyses. Results indicate a reduction in stature in the transition from the Iron Age to the Roman period, and a subsequent increase in the transition from the Roman period to the Medieval period. Changes of limb lengths over time were more pronounced in the distal than in the proximal elements in both limbs.     

Extant primitively segmented spiders have recently diversified from an ancient lineage

Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39–58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4–24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.     

The cell theory--history, present state and prospects (on the 150th anniversary of the development of the cell theory)

The main stages of history of this most important biological conception are presented and the state of the modern cell theory and its future prospects are considered. Since 1839, when T. Schwann expounded his conception of the cell, a long pathway in cognition of the cell function and organization has been covered. From the original picture of the complex organism as a "cellular state", made up of relatively independent "elementary organisms", i.e. cells the modern biology has come to the idea of the cell as an integral system either being a part of a complex organism, or living free in the nature (protists). The cell represents certain qualitatively peculiar level in a complex evolutionary established hierarchy of biological systems. Some particular tight relations, existing between cytology, as a fundamental biological science and molecular biology, genetics, ecology and other biological disciplines are considered. The importance of the cell conception is ascertained for practical aims, especially in medicine.     

Biological atomism and cell theory

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with the theory's conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology.     

A Posteriori: Getting to the Bottom of Human Development

This article asserts that the most important physical feature distinguishing man from all other creatures, one which allowed for and contributed to the development of the thumb and the brain, which facilitated and encouraged the development of his imagination, his ability to think abstractly and even to doubt, and made it possible for him to master all other life forms and advance so far in containing and even conquering some forces of nature is his well-developed posterior; superior to that of all other living creatures: while sitting comfortably for long periods freed his hands and vision, it also allowed him to imagine and ponder what was over the horizon.