Activity patterns in New Kingdom Nubia: An examination of entheseal remodeling and osteoarthritis at Tombos

The effects of Egyptian imperial expansion into Nubia during the New Kingdom Period (1,550–1,069 BC) have been debated. Here, the impacts of the Egyptian Empire are investigated through an examination of osteological indicators of activity at the archaeological site of Tombos. Entheseal changes to fibrocartilaginous attachment sites and osteoarthritis are examined to infer what types of physical activities this colonial town was engaging in. Many of the skeletal remains at Tombos were comingled due to looting in antiquity; undisturbed burials are presented as a subsample of the population (n = 28) in which age, sex, and body size can be considered. The total sample (n = 85) is then analyzed to better understand overall levels of activity. A number of Nile River Valley bioarchaeological samples are used as points of comparison to the Tombos population. Results indicate that the inhabitants of Tombos had relatively low entheseal remodeling scores; this is highlighted when Tombos is juxtaposed with comparative samples, particularly in men. Furthermore, osteoarthritis, as assessed by eburnation, was also markedly infrequent at Tombos. Collectively, these results indicate a relatively low level of activity and support the hypothesis that Tombos may have served as an administrative center. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.     

Health of the non-elites at Tombos: Nutritional and disease stress in New Kingdom Nubia

During the New Kingdom period, Egypt succeeded in occupying most of Nubia. Colonial towns were built, which served as centers of government and redistribution. This paper uses a bioarchaeological approach to address the effects of this cultural contact on non-elites. Skeletal remains from the site of Tombos (N = 100), a cemetery in Upper Nubia dating to this important time, are analyzed, in addition to 1,082 individuals from contemporaneous Egyptian and Nubian sites, in order to shed light on the social, political, and economic processes at play and to determine how the people at Tombos were affected during this transitional period. In many ways, the Tombos population appears to have been affected by similar stressors as the other populations under study. However, a few small differences in the subadult frequencies of pathological lesions, especially remodeling rates, are significant in the overall picture of health at Tombos. These analyses suggest that, although the people of Tombos may have been integrated into the Egyptian colonial network, the additional resources they may have obtained could not protect them from nutritional and disease stress. A lower childhood survival through bouts of ill health at Tombos is suggested. While status may have played a role in the differences seen in the comparative populations, it is likely that parasites and/or other infections led to childhood illness and death.     

Traumatic injuries and imperialism: the effects of Egyptian colonial strategies at Tombos in upper Nubia

As circumstances of conquest change, leaders of empires must adapt their colonial strategies in order to be successful. One example of such modification in approach is the shift from Middle Kingdom to New Kingdom Egyptian colonial activities in Nubia. During the Middle Kingdom (2050-1650 BC) Egypt used aggressive military campaigns to subdue the strong Nubian polity at Kerma, resulting in the construction of fortresses and many victory stelae. In the subsequent New Kingdom period (1550-1050 BC) during which the Egyptian administration succeeded in occupying nearly all of Nubia, changes were necessary in conquest strategies. Diplomacy and cooperation may have replaced military action as mechanisms of control. This article investigates changes in imperial policy through the examination of traumatic injuries in human skeletal remains. Patterns of injuries in a sample from the site of Tombos, an Egyptian colonial cemetery in Nubia dating to the New Kingdom period, are compared with data on the patterns of injuries from Kerma, a cemetery dating to the Middle Kingdom period, published by Judd (2004). Analysis indicates a decrease in the level of traumatic injuries from Kerma to Tombos supporting the idea that through time the Egyptian administration modified their colonial strategy toward more nonviolent means. This article presents data on differences in the patterns of injury at Tombos and Kerma and explores possible explanations for this variation.     

Methodological remarks on rearing basal Attini ants in the laboratory for biological and evolutionary studies: overview of the genus <Emphasis Type="Italic">Mycetophylax</Emphasis>

Some studies require fresh biological material for their development. Ant colonies have been reared under laboratory conditions for scientific purposes, and several methodologies for leafcutter ants have been reported in the literature. However, these methods are not well adapted for rearing basal Attini. In this study, we proposed a methodology for rearing basal Attini species in the laboratory based on the evaluation of colonies of the genus Mycetophylax. The complete system consists of two round translucent polypropylene containers inserted one inside the other, where one serves as a chamber proper and the other as a foraging area. Both containers are sealed with their lids, protecting the environment against desiccation. From a total of 29 colonies collected in the field, 22 colonies survived for at least 30 weeks, and Mycetophylax morschi was the most adapted for rearing under laboratory conditions. The main problem with rearing basal Attini in the laboratory is the loss of moisture. Thus, the method applied here may be adopted for rearing other basal Attini, as well as other ant species very sensitive to moisture variation.     

Efficiency of Phytoseiulus longipes Evans as a control agent of Tetranychus evansi Baker & Pritchard (Acari: Phytoseiidae: Tetranychidae) on screenhouse tomatoes

The spider mite Tetranychus evansi Baker & Pritchard can cause severe damage to tomato crops. The predatory mite Phytoseiulus longipes Evans was recently reported in association with T. evansi in Uruguaiana, Rio Grande do Sul State, Brazil. The objective of the present study was to evaluate the effects of P. longipes on the population of T. evansi on tomatoes under screenhouse condition. The study consisted on four experiments, in each of which 80 potted plantlets were distributed in two plots of 40 plantlets each. Two weeks later, each plantlet of both plots was infested with eight adult females of T. evansi; one week after, four adult females of P. longipes were released onto each plant of one plot. The population levels of T. evansi and the damage caused by these mites were significantly lower (P < 0.05; linear mixed-effect model) in the plots where P. longipes had been released. The results indicate the potential of this predator as a candidate for classical biological control of T. evansi by inoculative releases on tomato plants.     

Biophysical Reviews’ “Meet the Councilor”—a profile of Anastasia A. Anashkina

As one of the twelve Councilors of the International Union of Pure and Applied Biophysics elected in summer 2021, I have been asked to provide this short biographical sketch for the journal readers. I am a new member of the IUPAB Council. I hold a specialist degree in Applied Physics and Mathematics from the Moscow Institute of Physics and Technology and PhD in Biophysics from Moscow State University. I have spent my entire professional career at Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences in Moscow, where I am currently a senior researcher. I am Associate Professor at the Digital Health Institute of the I.M. Sechenov First Moscow State Medical University since 2018, and have trained undergraduate students in structural biology, biophysics, and bioinformatics. In addition, I serve as the Guest Editor of special journal issues of International Journal of Molecular Sciences and Frontiers in Genetics BMC genomics. Now I joined Biophysical Reviews Editorial Board as IUPAB Councilor. I am a Secretary of National Committee of Russian Biophysicists, and have helped to organize scientific conferences and workshops, such as the VI Congress of Russian Biophysicists.

     

Preparation and application of solvent‐modulated self‐doped N–S multicolour fluorescence carbon quantum dots

In this paper, two types of carbon quantum dot (CQDs) were prepared using biocompatible l ‐methionine as the carbon source and urea as the nitrogen source and a one‐step hydrothermal treatment. By changing the reaction solvents (deionized (DI) water and dimethylformamide (DMF)), the maximum emission of the resulting CQDs shifted from blue to red light. Specifically, the emission wavelength of the CQDs moved from 433 nm to 625 nm following embedding of a new functional group (–CONH–) on the surface of the CQDs. Photoluminescence quantum yields of the CQDs with blue and red emission reached 64% and 61%, respectively. The R‐CQDs were used to detect metal ions and a linear relationship was demonstrated between ln(F/F₀) and Fe³⁺ concentration in the range 0–0.5 mmol/L with a detection limit of 0.067 μM. Therefore these R‐CQDs have great potential as fluorescent probes for Fe³⁺ detection. We expect that the excellent water‐soluble, biocompatible and optical properties of the CQDs developed in this work mean that they will be widely used to detect biological cells.     

A revised account of initial mute swan (<Emphasis Type="Italic">Cygnus olor</Emphasis>) introductions to the northeastern United States

The success or failure of species introductions is linked to their location, date, size, and frequency. However, reliance on synthetic works to identify and quantify these factors can lead to errors if original sources are misinterpreted or misquoted. Furthermore, information cannot be verified if authors fail to cite their sources and repetition may lead to compounded errors that have implications for studies of invasion patterns and processes. Naturalized populations of mute swans (Cygnus olor) in the Atlantic Flyway, for example, are repeatedly attributed to two large introductions in New York State. Tracing this belief back to original reports and using additional historical records, this inquiry investigates the first introductions of mute swans in New York State and presents evidence for three initial sites. Newspapers are also recommended as a newly searchable archive of species introduction records.     

Quantum biology at the cellular level—Elements of the research program

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) – a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the ‘basis-dependent’ nature of these concepts. We introduce the notion of ‘formal superposition’ and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular ‘decision-making’ and adaptation. We stress that the interpretation of the notion of ‘formal superposition’ should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., ‘Basis-Dependent Selection’, BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the ‘evolvability mechanism’ loophole are also discussed.     

MtDNA markers reveal the existence of allopatric evolutionary lineages in the threatened lampreys <Emphasis Type="Italic">Lampetra fluviatilis</Emphasis> (L.) and <Emphasis Type="Italic">Lampetra planeri</Emphasis> (Bloch) in the Iberian glacial refugium

The Iberian Peninsula has been identified as an important glacial refugium during the Pliocene and Pleistocene epochs for the genus Lampetra, providing intermittent refuge and postglacial opportunities for colonization and expansion. We used mitochondrial DNA markers to investigate the processes that have shaped present-day genetic constitution of the genus Lampetra within the Iberian Peninsula. We surveyed 1,173 bp of the cytochrome b gene and 829 bp of the genes ATPase subunits 6 and 8 in 233 individuals of Lampetra fluviatilis (L.) and Lampetra planeri (Bloch) from 21 localities along their distribution range in the Iberian Peninsula. We identified four highly divergent allopatric evolutionary lineages that evolved by fragmentation during the Pliocene and Pleistocene likely driven by environmental factors, namely regional geomorphic events. The high level of genetic divergence between the four lineages suggests that sufficient time has apparently passed by to originate a complex of incipient or cryptic resident species and allows the definition of four evolutionary significant units (ESUs) for L. planeri and one ESU for L. fluviatilis. These findings have important consequences for the interpretation of refugia biological diversity and have major implications on the conservation of these threatened species.     

A biologist’s view of the relevance of thermodynamics and physical chemistry to cryobiology

Thermodynamics and physical chemistry have played powerful roles the past 45 years in interpreting cryobiological problems and in predicting cryobiological outcomes. The author has been guided by a few core principles in using these concepts and tools and this paper discusses these core principles. They are (1) the importance of chemical potentials and of the difference between the chemical potentials of water and solutes inside the cell and outside in determining the direction and rate of fluxes of water and solutes. (2) The influence of the curvature of an ice crystal on its chemical potential and on the ability of ice to pass through pores in cell membranes, on the nucleation temperature of supercooled water, and on the recrystallization of ice. (3) The use of Le Chatalier’s Principle in qualitatively predicting the direction of a reaction in response to variables like pressure. (4) The fact that the energy differences between State A and State B are independent of the path taken to go from A to B. (5) The importance of being aware of the assumptions underlying thermodynamic models of cryobiological events. And (6), the difficulties in obtaining experimental verification of thermodynamic and physical-chemical models.     

Probing the interaction of distamycin A with S100β: the “unexpected” ability of S100β to bind to DNA‐binding ligands

DNA‐minor‐groove‐binding ligands are potent antineoplastic molecules. The antibiotic distamycin A is the prototype of one class of these DNA‐interfering molecules that have been largely used in vitro. The affinity of distamycin A for DNA is well known, and the structural details of the complexes with some B‐DNA and G‐quadruplex‐forming DNA sequences have been already elucidated. Here, we show that distamycin A binds S100β, a protein involved in the regulation of several cellular processes. The reported affinity of distamycin A for the calcium(II)‐loaded S100β reinforces the idea that some biological activities of the DNA‐minor‐groove‐binding ligands arise from the binding to cellular proteins. Copyright © 2015 John Wiley & Sons, Ltd.     

The physical influence of inositides—a disproportionate effect?

After the initial observation that lipids form a considerable part of biological membranes, the details of the physical role of lipids in biological systems have emerged gradually. There have been few ‘Eureka’ moments in which a class or individual lipid has appeared as a game-changing physical player. However, evidence collected in the last five years suggests that that notion may be about to change. In chemical biology studies, inositides are increasingly showing themselves to be lipids that have a physical influence on membrane systems that is as strong as their biological (signalling) one. Additionally, recent evidence has shown that the concentration of at least one inositide changes during important stages of the cell cycle, and not in a manner consistent with its traditional signalling roles. The balance between these data is explored and a forward-looking view is proposed.     

The karyotype and 5S rRNA genes from Spanish individuals of the bat species <Emphasis Type="Italic">Rhinolophus</Emphasis><Emphasis Type="Italic">hipposideros</Emphasis> (Rhinolophidae; Chiroptera)

The karyotype of individuals of the species Rhinolophus hipposideros from Spain present a chromosome number of 2n = 54 (NFa = 62). The described karyotype for these specimens is very similar to another previously described in individual from Bulgaria. However, the presence of one additional pair of autosomal acrocentric chromosomes in the Bulgarian karyotype and the differences in X chromosome morphology indicated that we have described a new karyotype variant in this species. In addition, we have analyzed several clones of 1.4 and 1 kb of a PstI repeated DNA sequence from the genome of R. hipposideros. The repeated sequence included a region with high identity with the 5S rDNA genes and flanking regions, with no homology with GenBank sequences. Search for polymerase III regulatory elements demonstrated the presence of type I promoter elements (A-box, Intermediate Element and C-box) in the 5S rDNA region. In addition, upstream regulatory elements, as a D-box and Sp1 binding sequences, were present in flanking regions. All data indicated that the cloned repeated sequences are the functional rDNA genes from this species. Finally, FISH demonstrated the presence of rDNA in nine chromosome pairs, which is surprising as most mammals have only one carrier chromosome pair.     

Is hydrogen sulfide a circulating “gasotransmitter” in vertebrate blood?

Hydrogen sulfide (H₂S) is gaining acceptance as a signaling molecule and has been shown to elicit a variety of biological effects at concentrations between 10 and 1000 μmol/l. Dissolved H₂S is a weak acid in equilibrium with HS⁻ and S²⁻ and under physiological conditions these species, collectively referred to as sulfide, exist in the approximate ratio of 20% H₂S, 80% HS⁻ and 0% S²⁻. Numerous analyses over the past 8 years have reported plasma or blood sulfide concentrations also in this range, typically between 30 and 300 μmol/l, thus supporting the biological studies. However, there is some question whether or not these concentrations are physiological. First, many of these values have been obtained from indirect methods using relatively harsh chemical conditions. Second, most studies conducted prior to 2000 failed to find blood sulfide in micromolar concentrations while others showed that radiolabeled ³⁵S-sulfide is rapidly removed from blood and that mammals have a relatively high capacity to metabolize exogenously administered sulfide. Very recent studies using H₂S gas-sensing electrodes to directly measure sulfide in plasma or blood, or HPLC analysis of head-space gas, have also indicated that sulfide does not circulate at micromolar levels and is rapidly consumed by blood or tissues. Third, micromolar concentrations of sulfide in blood or exhaled air should be, but are not, malodorous. Fourth, estimates of dietary sulfur necessary to sustain micromolar levels of plasma sulfide greatly exceed the daily intake. Collectively, these studies imply that many of the biological effects of sulfide are only achieved at supra-physiological concentrations and they question whether circulating sulfide is a physiologically relevant signaling molecule. This review examines the blood/plasma sulfide measurements that have been reported over the past 30 years from the perspective of the analytical methods used and the potential sources of error.     

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.

This study describes a novel mechanistic engine that predicts a realistic global latitudinal diversity gradient, species richness distribution and phylogenies. This approach is a step towards the interdisciplinary numeric understanding of the physical and biological processes that have shaped Earth’s biodiversity.     

Pennsylvanian palynofloras from the Itu rhythmites (Itararé Subgroup, Paraná Basin) in São Paulo State, Brazil

The rhythmites of Itu present the best exposures of glacial varvites known in the Paraná Basin, and constitute a classic geological monument related to the Late Palaeozoic Gondwanan glaciation. Palynological results in this paper are based on rhythmites from two quarries in Itu area, central-eastern State of São Paulo, Brazil, including correlate levels of the “Itu Varvite Park”, as well as based on samples from the borehole IT-IG-85 (at 171 and 228 m) drilled also in the Itu City. Well-preserved indigenous miospores and microphytoplankton elements have been recorded. The former comprise 15 spore species and 19 pollen species, of which three are recorded for the first time in the Brazilian part of the Paraná Basin (Verrucosisporites cf. V. andersonii, Convolutispora archangelskyi and Caheniasaccites verrucosus). Microalgae include prasinophyceans (Leiosphaeridia sp., Tasmanites sp., Deusilites tenuistriatus), chlorophyceans (Botryococcus braunii) and zignemataceans (Tetraporina). The palynological content confirms a late Pennsylvanian (Kasimovian/Gzhelian) age for these rhythmites, which are assigned to the Crucisaccites monoletus interval Zone, based on the record of the eponymous pollen species and Scheuringipollenites maximus. Although very scarce, prasinophycean algae suggest low salinity marine conditions.