High-resolution isotopic evidence of specialised cattle herding in the European Neolithic.

Peer reviewe

The Basel-Gasfabrik research project: Addressing complex topics by an integrative approach

The late La Tène period site of Basel-Gasfabrik has been under investigation for more than a century. During that time, the unfortified settlement with its two cemeteries has yielded huge amounts of everyday and exceptional objects and features. Beginning in the mid-1970s, samples were systematically collected for scientific analyses during ongoing excavations, thus producing ideal preconditions for interdisciplinary research. In 2011-2014, the international research project “Approaching the living via the dead: human remains from the Late La Tène site Basel-Gasfabrik and their cultural-historical interpretations” addressed the multifarious ways in which the Iron Age community handled their deceased. The intense collaboration involved researchers from the Archäologische Bodenforschung Basel-Stadt and the universities of Basel (CH), Mainz and Freiburg i.Br. (D) and spanned eight disciplines: archaeology, archeoanthropology, archaeobotany, archaeozoology, geoarchaeology, biogeochemistry, molecular genetics and statistics. Research topics and theoretical frameworks were developed jointly as well as procedures to combine the disciplinary results in multistage processes in order to generate integrative syntheses of novel insights. The challenges and specific research potentials of the integrative approach may serve as a positive example for future interdisciplinary research project

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

Activating PER Repressor through a DBT-Directed Phosphorylation Switch

Protein phosphorylation plays an essential role in the generation of circadian rhythms, regulating the stability, activity, and subcellular localization of certain proteins that constitute the biological clock. This study examines the role of the protein kinase Doubletime (DBT), a Drosophila ortholog of human casein kinase I (CKI)ɛ/δ. An enzymatically active DBT protein is shown to directly phosphorylate the Drosophila clock protein Period (PER). DBT-dependent phosphorylation sites are identified within PER, and their functional significance is assessed in a cultured cell system and in vivo. The perS mutation, which is associated with short-period (19-h) circadian rhythms, alters a key phosphorylation target within PER. Inspection of this and neighboring sequence variants indicates that several DBT-directed phosphorylations regulate PER activity in an integrated fashion: Alternative phosphorylations of two adjoining sequence motifs appear to be associated with switch-like changes in PER stability and repressor function

On-site data cast doubts on the hypothesis of shifting cultivation in the Late Neolithic (c. 4300-2400 cal. BC): Landscape management as an alternative paradigm

This article brings together in a comprehensive way, and for the first time, on- and off-site palaeoenvironmental data from the area of the Central European lake dwellings (a UNESCO World Cultural Heritage Site since 2011). The types of data considered are as follows: high-resolution off-site pollen cores, including micro-charcoal counts, and on-site data, including botanical macro- and micro-remains, hand-collected animal bones, remains of microfauna, and data on woodland management (dendrotypology). The period considered is the late Neolithic (c. 4300–2400 cal. BC). For this period, especially for its earlier phases, discussions of land-use patterns are contradictory. Based on off-site data, slash-and-burn – as known from tropical regions – is thought to be the only possible way to cultivate the land. On-site data however show a completely different picture: all indications point to the permanent cultivation of cereals (Triticum spp., Hordeum vulgare), pea (Pisum sativum), flax (Linum usitatissimum) and opium-poppy (Papaver somniferum). Cycles of landscape use are traceable, including coppicing and moving around the landscape with animal herds. Archaeobiological studies further indicate also that hunting and gathering were an important component and that the landscape was manipulated accordingly. Late Neolithic land-use systems also included the use of fire as a tool for opening up the landscape. Here we argue that bringing together all the types of palaeoenvironmental proxies in an integrative way allows us to draw a more comprehensive and reliable picture of the land-use systems in the late Neolithic than had been reconstructed previously largely on the basis of off-site data

Regulation of Clock-Controlled Genes in Mammals

The complexity of tissue- and day time-specific regulation of thousands of clock-controlled genes (CCGs) suggests that many regulatory mechanisms contribute to the transcriptional output of the circadian clock. We aim to predict these mechanisms using a large scale promoter analysis of CCGs

An initial comparative map of copy number variations in the goat (Capra hircus) genome

<p>Abstract</p> <p>Background</p> <p>The goat (<it>Capra hircus</it>) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.</p> <p>Results</p> <p>We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P < 0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals.</p> <p>Conclusions</p> <p>We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.</p

LIPH Expression in Skin and Hair Follicles of Normal Coat and Rex Rabbits

Natural mutations in the LIPH gene were shown to be responsible for hair growth defects in humans and for the rex short hair phenotype in rabbits. In this species, we identified a single nucleotide deletion in LIPH (1362delA) introducing a stop codon in the C-terminal region of the protein. We investigated the expression of LIPH between normal coat and rex rabbits during critical fetal stages of hair follicle genesis, in adults and during hair follicle cycles. Transcripts were three times less expressed in both fetal and adult stages of the rex rabbits than in normal rabbits. In addition, the hair growth cycle phases affected the regulation of the transcription level in the normal and mutant phenotypes differently. LIPH mRNA and protein levels were higher in the outer root sheath (ORS) than in the inner root sheath (IRS), with a very weak signal in the IRS of rex rabbits. In vitro transfection shows that the mutant protein has a reduced lipase activity compared to the wild type form. Our results contribute to the characterization of the LIPH mode of action and confirm the crucial role of LIPH in hair production

Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems

Mesoscopic oscillatory reaction systems, for example in cell biology, can exhibit stochastic oscillations in the form of cyclic random walks even if the corresponding macroscopic system does not oscillate. We study how the intrinsic noise from molecular discreteness influences the frequency spectrum of mesoscopic oscillators using as a model system a cascade of coupled Brusselators away from the Hopf bifurcation. The results show that the spectrum of an oscillator depends on the level of noise. In particular, the peak frequency of the oscillator is reduced by increasing noise, and the bandwidth increased. Along a cascade of coupled oscillators, the peak frequency is further reduced with every stage and also the bandwidth is reduced. These effects can help understand the role of noise in chemical oscillators and provide fingerprints for more reliable parameter identification and volume measurement from experimental spectra

A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception

Evolution during millions of years in perpetual darkness leads to mutations in non-visual opsin genes (Melanopsin and TMT opsin) and an aberrant, blind circadian clock in cavefish