A new research strategy for integrating studies of paleoclimate,paleoenvironment, and paleoanthropology

Paleoanthropologists (scientists studying human origins) universally recognize the evolutionary significance of ancient climates and environments for understanding human origins. 1 - 6 Even those scientists working in recent phases of human evolution, when modern humans evolved, agree that hunter‐gatherer adaptations are tied to the way that climate and environment shape the food and technological resource base. 7 - 10 The result is a long tradition of paleoanthropologists engaging with climate and environmental scientists in an effort to understand if and how hominin bio‐behavioral evolution responded to climate and environmental change. Despite this unusual consonance, the anticipated rewards of this synergy are unrealized and, in our opinion, will not reach potential until there are some fundamental changes in the way the research model is constructed. Discovering the relation between climate and environmental change to human origins must be grounded in a theoretical framework and a causal understanding of the connection between climate, environment, resource patterning, behavior, and morphology, then move beyond the strict correlative research that continues to dominate the field.     

微生物学教学中人文教育渗透素材的选择

在微生物学课堂上渗透人文教育是微生物学教学改革的必然选择途径之一。微生物学包含着丰富的人文教育素材,这些内容包括古代典籍、历史事件、科学家传记、微生物学发展史、新闻热点等。合理应用这些素材可以提升课堂的文化氛围,提高学生的学习兴趣,并引导学生形成正确的人生观、世界观和价值观。     

古DNA 及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA。本文回顾了近20年古DNA研究所经历的3个阶段, 从早期参与研究的科学家较少并主要利用克隆技术, 到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道; 近几年由于发现不少问题, 并引起激烈的争论, 科学家们因此而开始考虑古DNA的真实性问题, 并且提出了开展古DNA研究的严格标准。本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状, 表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据, 也对某些观点提出了挑战; 古DNA研究还提供了某些已经灭绝生物的形态学和分子资料, 为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据。在动植物驯化及考古方面, 古DNA证据也为科学家提供了许多有价值的信息。最后, 本文还对古DNA研究的应用前景进行了展望。     

Acupuncture: it take the pain away?

Acupuncture is growing in popularity in most Western countries and continues to be a major form of medicine in China and Japan. In the USA, an estimated ten million consultations for acupuncture take place each year. Many scientists regard acupuncture, like many other ‘alternative’ therapies, as an over-dressed placebo that fulfills a need for mysticism and ancient ritual. But if we dismiss acupuncture in this way, are we rejecting an opportunity to learn more about the body's response to pain?     

古DNA及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA.本文回顾了近20年古DNA研究所经历的3个阶段,从早期参与研究的科学家较少并主要利用克隆技术,到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道;近几年由于发现不少问题,并引起激烈的争论,科学家们因此而开始考虑古DNA的真实性问题,并且提出了开展古DNA研究的严格标准.本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状,表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据,也对某些观点提出了挑战;古DNA研究还提供了某些已经灭绝生物的形态学和分子资料,为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据.在动植物驯化及考古方面,古DNA证据也为科学家提供了许多有价值的信息.最后,本文还对古DNA研究的应用前景进行了展望.     

古DNA提取技术新进展

古DNA是揭示古代生物生长状态以及生物千百万年来进化情况的最重要的信息载体,在治疗人类遗传性的疑难病症及牲畜饲养和粮食作物种植等方面都有重大的贡献。古DNA提取技术作为获得该重要的信息载体的最重要手段,长久以来受到了世界各地的考古学家以及医学研究学者们的高度重视。随着科学的发展,古DNA提取技术已经形成多种核心方法:Chelex-100法、酚-氯仿抽提法、二氧化硅(硅粒)法、NaOH法、硅离心柱法试剂盒、磁珠法试剂盒等方法。本文将根据最新的研究成果对以上提到的几种方法进行分析比较,以期能够为将来古DNA提取技术的发展创新提供新的思路与方向。     

古DNA提取技术新进展

古DNA 是揭示古代生物生长状态以及生物千百万年来进化情况的最重要的信息载体,在治疗人类遗传性的疑难病症及牲畜饲养和粮食作物种植等方面都有重大的贡献。古DNA提取技术作为获得该重要的信息载体的最重要手段,长久以来受到了世界各地的考古学家以及医学研究学者们的高度重视。随着科学的发展,古DNA提取技术已经形成多种核心方法：Chelex-100 法、酚-氯仿抽提法、二氧化硅（硅粒）法、NaOH 法、硅离心柱法试剂盒、磁珠法试剂盒等方法。本文将根据最新的研究成果对以上提到的几种方法进行分析比较,以期能够为将来古DNA提取技术的发展创新提供新的思路与方向。     

Ancient DNA studies

Now that the hype surrounding Jurassic Park has settled down and we have become relatively used to dramatic headlines announcing the recovery of DNA from exotic fossilized remains, scientists working on ancient DNA are beginning to reflect on the long-term prospects and implications of the subject.¹ The science of ancient DNA has grown exponentially since its birth only ten years ago, and despite serious technical difficulties, it promises to become a revolutionary research tool in anthropology and molecular evolution. The use of bone DNA typing in particular has already yielded useful insights into Polynesian prehistory as well as spectacular applications in the forensic identification of skeletal remains.     

Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene,Italy

Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep‐sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north‐eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910–5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo‐reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.     

Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia

Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.     

Relationship between cancer and psychology: an updated history

The mechanism and formation of cancer have always been topics of interest for scientists, even for doctors in ancient times. Nowadays a great role for cancer is played by psychological stress which promotes relevant changes in neuronal activity and gene regulations across the different brain areas. It has been reported by many authors that stress can have an important role in the immune system and may be relevant in the formation of cancer. Our observations, in accordance with other research studies, confirm the importance of the influence of depression, linked to neuroendocrine stress, on the enhancement of cancer pathogenesis by inhibiting anti-tumor immune responses. In this article we review the past and present history of the relationship between cancer and psychology.     

Polygenic inheritance of bean mass

Analogies between plants and animals are often a source of confusion in the understanding of sexual reproduction in green plants

The ancient view that plants are non-sexual because they hold a place below animals on the ladder of nature was still held by many scientists in the 1 8th century. Paradoxically, al this time, Linnaeus and others were also postulating the universality of plant sexuality by using analogies with animals to over-extend the slowly emerging experimental evidence about the functions of floral parts. Today's school leavers seem to have similarly diverse views. A lack of school focus on gamete fusion appears to result in a continuing reliance on analogies with animals, and a belief that plants undergo only a qualified version of sexual reproduction. Suggestions for classroom activities to overcome this are offered, and some wider implications are considered.     

The discovery of the body: human dissection and its cultural contexts in ancient Greece.

In the first half of the third century B.C, two Greeks, Herophilus of Chalcedon and his younger contemporary Erasistratus of Ceos, became the first and last ancient scientists to perform systematic dissections of human cadavers. In all probability, they also conducted vivisections of condemned criminals. Their anatomical and physiological discoveries were extraordinary. The uniqueness of these events presents an intriguing historical puzzle. Animals had been dissected by Aristotle in the preceding century (and partly dissected by other Greeks in earlier centuries), and, later, Galen (second century A.D.) and others again systematically dissected numerous animals. But no ancient scientists ever seem to have resumed systematic human dissection. This paper explores, first, the cultural factors--including traditional Greek attitudes to the corpse and to the skin, also as manifested in Greek sacred laws--that may have prevented systematic human dissection during almost all of Greek antiquity, from the Pre-Socratic philosopher-scientists of the sixth and fifth centuries B.C. to distinguished Greek physicians of the later Roman Empire. Second, the exceptional constellation of cultural, political, and social circumstances in early Alexandria that might have emboldened Herophilus to overcome the pressures of cultural traditions and to initiate systematic human dissection, is analyzed. Finally, the paper explores possible reasons for the mysteriously abrupt disappearance of systematic human dissection from Greek science after the death of Erasistratus and Herophilus.     

Is It Human? Discriminating between Real Tracks and Track-Like Structures

Some human footprints-like hollows in the tuffaceous ground of an ancient quarry and of a recent anthropic path, created by the inhabitants no more than 30 years ago near the small village of Carangi (Caserta province, Southern Italy), allowed scientists to study some of the most misleading alteration processes of the volcanic tuff formations. The closeness of this site to the “Ciampate del Diavolo” ichnosite, bearing some of the oldest human fossil footprints, and the common stratigraphical and sedimentological background permitted accurate comparisons between actual human fossil footprints and footprint-like depressions, which can be easily mistaken for actual fossil evidence. This comparative study has permitted the reporting of some useful features and advice on distinguishing actual fossil footprints from natural and/or anthropic pseudo-tracks.     

The Swiss archaeologist Otto Hauser. His skeletal findings and hypothesis on the evolution of man and his extensive activities in the development of prehistorical research and evolution

New investigations on Otto Hauser's skeleton findings and the excavations of this Swiss citizen in Southwest France from 1906 until 1914 placed the activities of this archaeologist again in the focus of scientific and public interest. This paper describes life and oeuvre of Otto Hauser and discusses the importance of the skeletons found by him and Hermann Klaatsch as well as the consequences of their discovery. The efforts of Otto Hauser to publish his discoveries, to present and spread his view concerning the evolution of man were remarkably manifold as well as the parallels between ancient man and contemporary ethnic groups living on a low technological level drawn by him and to wake and to promote the interest in prehistory. Many books, brochures, articles and public lectures contributed to this intention as well as co-operation with local historians and scientists of other disciplines, and also many films, teaching and illustrative materials. The scientific collection of the authors of this article comprises more than 6,500 written documents and photos.     

On the conceptual difficulties in rooting the tree of life

Rooting the 'tree of life' represents a major challenge for evolutionists. Without such a root, many of the first steps in biological evolution cannot be reconstructed. However, the nature of the last common ancestor of all living beings remains elusive, proof of the difficulty in shedding light on such an ancient event. Here, we highlight the practical difficulties and conceptual reasons that hinder the placement of a universal root. We discuss how, when addressing the question of the root of the tree of life, scientists unconsciously risk using the reasoning pattern of ancient skeptics, unfortunately known only to lead to further uncertainty. Hence, we argue that the root of the tree of life will not be established unless radically new approaches are considered. We propose a hypothetical means to overcome several of the conceptual difficulties pointed out, and suggest that a so-called 'transition analysis' of the structural evolution of the cytoplasmic membrane might be helpful, especially if evolutionary steps involving the rooting issue are polarized accounting more for physicochemical knowledge rather than hypothetical and controversial selective advantages.     

When galectins recognize glycans: from biochemistry to physiology and back again

In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings.     

Trade-off between light availability and soil fertility determine refugial conditions for the relict light-demanding species in lowland forests

Identifying potential refugial habitats in the face of rapid environmental change is a challenge faced by scientists and nature conservation managers. Relict populations and refugial habitats are the model objects in those studies. Based on the example of Actaea europaea from Central Poland, we analyse the habitat factors influencing relict populations of continental, light-demanding species in lowland forests and examine which habitats of studied species corresponding most closely to ancient vegetation. Our results indicate that the current refugial habitats of Actaea europaea include not only communities which are very similar to ancient open forest but also forests with a closed canopy. Although the populations are influenced by nitrogen and light availability, the co-occurrence of these two factors in forest communities is limited by dense canopy formation by hornbeam and beech trees on fertile soils and in more humid conditions. Our findings indicate that the future survival of relict, light-demanding communities in lowland forests requires low-intensity disturbances to be performed in tree-stands, according to techniques, which imitate traditional forests management.     

Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling

Background

The classification of ancient animal corpses at the species level remains a challenging task for forensic scientists and anthropologists. Severe damage and mixed, tiny pieces originating from several skeletons may render morphological classification virtually impossible. Standard approaches are based on sequencing mitochondrial and nuclear targets.

Methodology/Principal Findings

We present a method that can accurately classify mammalian species using dental pulp and mass spectrometry peptide profiling. Our work was organized into three successive steps. First, after extracting proteins from the dental pulp collected from 37 modern individuals representing 13 mammalian species, trypsin-digested peptides were used for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. The resulting peptide profiles accurately classified every individual at the species level in agreement with parallel cytochrome b gene sequencing gold standard. Second, using a 279–modern spectrum database, we blindly classified 33 of 37 teeth collected in 37 modern individuals (89.1%). Third, we classified 10 of 18 teeth (56%) collected in 15 ancient individuals representing five mammal species including human, from five burial sites dating back 8,500 years. Further comparison with an upgraded database comprising ancient specimen profiles yielded 100% classification in ancient teeth. Peptide sequencing yield 4 and 16 different non-keratin proteins including collagen (alpha-1 type I and alpha-2 type I) in human ancient and modern dental pulp, respectively.

Conclusions/Significance

Mass spectrometry peptide profiling of the dental pulp is a new approach that can be added to the arsenal of species classification tools for forensics and anthropology as a complementary method to DNA sequencing. The dental pulp is a new source for collagen and other proteins for the species classification of modern and ancient mammal individuals.     

Empirical evaluation of bone extraction protocols

The application of high-resolution analytical techniques to characterize ancient bone proteins requires clean, efficient extraction to obtain high quality data. Here, we evaluated many different protocols from the literature on ostrich cortical bone and moa cortical bone to evaluate their yield and relative purity using the identification of antibody-antigen complexes on enzyme-linked immunosorbent assay and gel electrophoresis. Moa bone provided an ancient comparison for the effectiveness of bone extraction protocols tested on ostrich bone. For the immunological part of this study, we focused on collagen I, osteocalcin, and hemoglobin because collagen and osteocalcin are the most abundant proteins in the mineralized extracellular matrix and hemoglobin is common in the vasculature. Most of these procedures demineralize the bone first, and then the remaining organics are chemically extracted. We found that the use of hydrochloric acid, rather than ethylenediaminetetraacetic acid, for demineralization resulted in the cleanest extractions because the acid was easily removed. In contrast, the use of ethylenediaminetetraacetic acid resulted in smearing upon electrophoretic separation, possibly indicating these samples were not as pure. The denaturing agents sodium dodecyl sulfate, urea, and guanidine HCl have been used extensively for the solubilization of proteins in non-biomineralized tissue, but only the latter has been used on bone. We show that all three denaturing agents are effective for extracting bone proteins. One additional method tested uses ammonium bicarbonate as a solubilizing buffer that is more appropriate for post-extraction analyses (e.g., proteomics) by removing the need for desalting. We found that both guanidine HCl and ammonium bicarbonate were effective for extracting many bone proteins, resulting in similar electrophoretic patterns. With the increasing use of proteomics, a new generation of scientists are now interested in the study of proteins from not only extant bone but also from ancient bone.