Biological archaeology

Zooarkeoloji hem arkeolojinin en temel yöntemlerinden biri, hem de özgün teori ve tartışma konuları üretmiş başlı başına bir bilim dalıdır. Zooarkeolojinin başlıca malzemesi olan hayvan kalıntıları, Türkiye, Güneybatı Asya ve Balkanlar'daki tüm kazılardan bol miktarda elde edilir. Zooarkeoloji beslenmeden ritüele, iklimden stratigrafiye, mamut türlerinin neslinin tükenmesinden Osmanlı İmparatorluğu'nun ekonomik etkilerine kadar arkeolojinin ilgilendiği pek çok konuya ışık tutan çalışmalar yapar. Bunun yanı sıra, hayvanların evrimi, hayvan topluluklarının değişen dağılım alanları gibi biyolojik konuları aydınlatabilen pek az bilim dalından biridir. Bu bölümde zooarkeoloji en son gelişmeler de dahil olmak üzere ana hatlarıyla tanıtılacaktır.

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Infant care and nutrition in the Late Pleistocene represent a significant research area for understanding the effects of social and biological dynamics on child-rearing during a critical stage in human evolution. This study aims to investigate infant feeding practices, breastfeeding duration, and early life care practices in hunter-gatherer societies. Drawing on archaeological evidence, biomolecular analyses and anthropological data, the relationship of late Pleistocene childcare to social organization and survival strategies will be discussed.

Geç Pleistosen Çağ’da bebek bakımı ve beslenme, insan evriminin kritik bir evresinde toplumsal ve biyolojik dinamiklerin çocuk yetiştirme üzerindeki etkilerini anlamak açısından önemli bir araştırma alanı sunar. Bu çalışma, avcı-toplayıcı toplumlarda bebeklerin beslenme biçimlerini, emzirme sürelerini ve erken yaşam dönemlerindeki bakım uygulamalarını incelemeyi amaçlamaktadır. Arkeolojik buluntular, biyomoleküler analizler ve antropolojik veriler ışığında, Geç Pleistosen çocuk bakımının toplumsal organizasyon ve hayatta kalma stratejileriyle olan ilişkisi tartışılacaktır.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research. IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio-and experimental archaeology that aim to reconstruct ancient artifacts and products. KEYWORDS ancient fermented food and beverages, ancient pottery vessels, beer, bio-archaeology, experimental archaeology, yeasts E xperimental archaeology is a field of research that studies ancient cultures by trying to reconstruct ancient lifestyles, including tools, housing, clothing, and diet (1, 2). Among the most challenging subjects of study in this field are fermented food products, such as cheese and pickles, and alcoholic beverages, including wine, beer, and mead (honey wine). All of these products played important roles in ancient

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research. IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio-and experimental archaeology that aim to reconstruct ancient artifacts and products. KEYWORDS ancient fermented food and beverages, ancient pottery vessels, beer, bio-archaeology, experimental archaeology, yeasts E xperimental archaeology is a field of research that studies ancient cultures by trying to reconstruct ancient lifestyles, including tools, housing, clothing, and diet (1, 2). Among the most challenging subjects of study in this field are fermented food products, such as cheese and pickles, and alcoholic beverages, including wine, beer, and mead (honey wine). All of these products played important roles in ancient

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide modern microorganisms as a new tool in bio-archeology. So far, most of the study of ancient organisms was based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms, yeast in this case, from thousands of years old clay vessels, used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains which participated in the fermentation process and were absorbed into the pottery vessels. Moreover, we characterize the isolated yeast their genome and the beer they produce. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio and experimental -archeology that aims to reconstruct ancient artifacts and products.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research. IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio-and experimental archaeology that aim to reconstruct ancient artifacts and products. KEYWORDS ancient fermented food and beverages, ancient pottery vessels, beer, bio-archaeology, experimental archaeology, yeasts E xperimental archaeology is a field of research that studies ancient cultures by trying to reconstruct ancient lifestyles, including tools, housing, clothing, and diet (1, 2). Among the most challenging subjects of study in this field are fermented food products, such as cheese and pickles, and alcoholic beverages, including wine, beer, and mead (honey wine). All of these products played important roles in ancient

Kveik is the common name of yeast that has been used in traditional farmhouse brewing of western Norway for generations. Its fast fermentation, increased flocculation, temperature tolerance, and rich flavor profile have led to growing interest in recent years. Previous genetic analyses have shown that kveik forms a distinct group within the Saccharomyces cerevisiae tree and placed its origins within the Beer I clade of industrial brewing yeasts, although with signs of mixed ancestry. In this study, we revisited the phylogenetic position of kveik within the S. cerevisiae tree. We searched for traditional farm breweries in western Norway and collected ten samples of potential kveik yeast. .

New Zealand's National Isotope Centre, including the Rafter Radiocarbon Laboratory, has upgraded its AMS system from a 6 MV EN-Tandem AMS to a new generation 0.5 MV NEC Extended Compact AMS (XCAMS) system. Current precisions represent approximately an order of magnitude improvement during the AMS era-from 1-2% more than 20 years ago to $0.2% today. The year since 14 C operations were shifted from the EN-Tandem to XCAMS has seen a 40% increase in 14 C measurements without reaching full capacity of the new AMS system. Increased throughput and precision require improvements to systems used for the preparation of samples and reporting of results. Our approaches to these challenges are outlined here. They include the development of an automated combustion and CO 2 collection system, and consideration of sources of error or bias including calibration and background correction. Monitoring for any observable changes in reported values associated with the transfer from the EN-Tandem to XCAMS has also been a high priority, and no issues with the continuity of AMS results have been identified.

Turkiye'nin Harpacteinae faunasini belirlemeye yonelik yapilan arazi calismalarinda daha evvel erkek bireyler uzerinden betimlenen Harpactea erseni ve H . pugio turlerine ait ilave ornekler toplanmis; her iki turun de taksonomik karakterlerini olusturan erkek ve disi bireylerinin ureme organlarina ait ayrintili fotograflar verilmis, betimlemeler yapilmis ve turlerin dagilimi harita uzerinde gosterilmistir. H . erseni , erkek ureme organi ve bazi diger karakterleri itibariyla, cins icin tanimlanan rubicunda (D) tur grununa dahildir. Bununla birlikte yeni betimlenen disi ureme organi, posteriyor spermatekasinin tamamiyla sklerotize olmasi sebebiyle, lepida (C) tur grubu ile yakinlik gostermektedir. Bu durum makale icerisinde tartisilmistir. H . pugio , disi ureme organinin posteriyor spermatekasinda yer alan zarsi yapidaki posteriyor divertikulum ve her iki eseyinin sahip oldugu taksonomik karakterlerden dolayi rubicunda (D) tur grubu icerisinde degerlendirilmistir

New Zealand's National Isotope Centre, including the Rafter Radiocarbon Laboratory, has upgraded its AMS system from a 6 MV EN-Tandem AMS to a new generation 0.5 MV NEC Extended Compact AMS (XCAMS) system. Current precisions represent approximately an order of magnitude improvement during the AMS era-from 1-2% more than 20 years ago to $0.2% today. The year since 14 C operations were shifted from the EN-Tandem to XCAMS has seen a 40% increase in 14 C measurements without reaching full capacity of the new AMS system. Increased throughput and precision require improvements to systems used for the preparation of samples and reporting of results. Our approaches to these challenges are outlined here. They include the development of an automated combustion and CO 2 collection system, and consideration of sources of error or bias including calibration and background correction. Monitoring for any observable changes in reported values associated with the transfer from the EN-Tandem to XCAMS has also been a high priority, and no issues with the continuity of AMS results have been identified.

▪Overall, subadult age had little bearing on experienced analysts' abilities to identify correct pair matches ▪Diaphysis length, epiphyseal fusion, torsion, and muscle insertion sites were more confidently pair matched in most subadult groups compared to the adult humeri test, due to fewer subadult asymmetrical differences This research impacts anthropologists conducting identification projects with CHR. As commingled individuals with unfused and fusing epiphyses are encountered in various contexts 1, 4, 5, 6 this research indicates that experienced analysts can pair match subadult remains >1 year of age with 100% accuracy. Diminished morphological variability among long bones of 0-1 year suggests analysts should increase caution when assigning pair matches to individuals <1 year old

The recent announcement by Dr. Lee Berger and the team was a big surprise to many, less so to some, and even more controversial to others. As the first of multiple big announcements about naledi that we are expecting, we can examine the new claims and see what their effects on our understanding of what it means to be human could be.

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Norwegian kveik are a recently described family of domesticated Saccharomyces cerevisiae brewing yeasts used by farmhouse brewers in western Norway for generations to produce traditional Norwegian farmhouse ale. Kveik ale yeasts have been domesticated by farmhouse brewers through serial repitching of the yeast in warm wort (&gt;30°C) punctuated by long periods of dry storage. Kveik yeasts are alcohol tolerant, flocculant, capable of utilizing maltose/maltotriose, phenolic off flavour negative, and exhibit elevated thermotolerance when compared to other modern brewer’s yeasts belonging to the ‘Beer 1’ clade. However, the optimal fermentation and growth temperatures (Topt) for kveik ale yeasts and the influence of fermentation temperature of the production of flavour-active metabolites like fusel alcohols and sulfur compounds (H2S, SO2) are not known. Here we show that kveik ale yeasts have an elevated optimal fermentation temperature (Topt) when compared to commercial American Ale ye...

Norwegian kveik are a recently described family of domesticated Saccharomyces cerevisiae brewing yeasts used by farmhouse brewers in western Norway for generations to produce traditional Norwegian farmhouse ale. Kveik ale yeasts have been domesticated by farmhouse brewers through serial repitching of the yeast in warm wort (&gt;30°C) punctuated by long periods of dry storage. Kveik yeasts are alcohol tolerant, flocculant, capable of utilizing maltose/maltotriose, phenolic off flavour negative, and exhibit elevated thermotolerance when compared to other modern brewer’s yeasts belonging to the ‘Beer 1’ clade. However, the optimal fermentation and growth temperatures (Topt) for kveik ale yeasts and the influence of fermentation temperature of the production of flavour-active metabolites like fusel alcohols and sulfur compounds (H2S, SO2) are not known. Here we show that kveik ale yeasts have an elevated optimal fermentation temperature (Topt) when compared to commercial American Ale ye...

Ancient fermented food has been studied based on recipes, residue analysis and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach. We hypothesize that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and the descendants of these yeast could be isolated and studied long after. To this end, using a pipeline of yeast isolation from clay vessels developed here, we screened for yeast cells in beverage-related and non-related ancient vessels and sediments, from several archeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. Genomic analysis revealed that these yeast are similar to those found in traditional African beverages. Phenotypically, they grow similar to modern-beer producing yeast. Both strongly suggesting that they are descendants of the original fermenting yeast. These findings provide...

Els isòtops d&#x27;un element químic són àtoms que comparteixen el mateix nombre de protons però divergeixen en el de neutrons (tenen masses atòmiques diferents). Als isòtops amb una massa major se&#x27;ls anomena pesats (pe, 13C, 15N), i als que tenen una massa menor, ...

Homologous sequence alignments contain important information about the constraints that shape protein family evolution. Correlated changes between different residues, for instance, can be highly predictive of physical contacts within three-dimensional structures. Detecting such co-evolutionary signals via direct coupling analysis is particularly challenging given xsthe shared phylogenetic history and uneven sampling of different lineages from which protein sequences are derived. Current best practices for mitigating such effects include sequence-identity-based weighting of input sequences and post-hoc re-scaling of evolutionary coupling scores. However, numerous weighting schemes have been previously developed for other applications, and it is unknown whether any of these schemes may better account for phylogenetic artifacts in evolutionary coupling analyses. Here, we show across a dataset of 150 diverse protein families that the current best practices out-perform several alternativ...

We chose yeast as a model organism to explore how eukaryotic cells respond to heat stress. This study provides details on the way yeast responds to temperature changes and is therefore an empirical reference for basic cell research and industrial fermentation of yeast. We use the Qlucore Omics Explorer (QOE) bioinformatics software to analyze the gene expression profiles of the heat stress from Gene Expression Omnibus (GEO). Genes and their expression are listed in heat maps, and the gene function is analyzed against the biological processes and pathways. We can find that the expression of genes changed over time after heat stress. Gene expression changed rapidly from 0 min to 60 min after heat shock, and gene expression stabilized between 60 min to 360 min. The yeast cells begin to adjust themselves to the high temperatures in terms of the level of gene expression at about 60 min. In all of the involved pathways and biological processes, those related to ribosome and nucleic acid m...

At least 25% of patients with positive Candida albicans bloodstream infection also have one or more bacterial species associated with the infection. These polymicrobial infections are usually caused by coagulase-negative staphylococci, most commonly Staphylococcus epidermidis and are associated with significantly worse clinical outcomes as compared to monomicrobial infections. Here we show bacteria are present in C. albicans cultures started from isolated single colony platting. These co-evolving bacteria can only be detected by the use of specific selective medium and/or long periods of incubation from 8 days up to 48 weeks (approximately 4,000 generations), used in experimental evolution methods. The detection of these co-evolving bacteria is highly dependent on the type of enzyme used for 16S rRNA gene amplification and is often missed in clinical laboratory analysis because of short incubation periods, media and temperatures, used in mycology clinical routine, that are unfavorab...

ABSTRACTFermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here we show that during the repeated colonization of cheese, phenotypic and metabolomic traits of wild Penicillium molds rapidly change to produce mutants with properties similar to industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wild Penicillium strains serially passaged on cheese resulted in the reduction or complete loss of pigment, spore, and mycotoxin production. Mutants also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g. ge...

Domestication of plants and animals is the foundation for feeding the world population. We report that domestication of the model yeast S. cerevisiae reprogrammed its life cycle entirely. We tracked growth, gamete formation and cell survival across many environments for nearly 1000 genome sequenced isolates and found a remarkable dichotomy between domesticated and wild yeasts. Wild yeasts near uniformly trigger meiosis and sporulate when encountering nutrient depletions, whereas domestication relaxed selection on sexual reproduction and favoured survival as quiescent cells. Domestication also systematically enhanced fermentative over respiratory traits while decreasing stress tolerance. We show that this yeast domestication syndrome was driven by aneuploidies and gene function losses that emerged independently in multiple domesticated lineages during the specie’s recent evolutionary history. We found domestication to be the most dramatic event in budding yeast evolution, raising que...

A fraction of the most valuable bioactive compounds in beer comes from hop&#39;s polyphenols, mainly flavonoids, some of which are unique to inflorescences of that flowering plant. Although far from pharmacologically relevant concentrations, the intake of low doses of xanthohumol and related prenylflavonoids found in beer contributes to significant preventive actions with regards to certain diseases, such as cardiovascular and neurodegenerative, as well as to distinct chemopreventive effects on certain cancer types. Hence the efforts to explore both ingredients and methods able to enhance the concentration of such bioactive compounds in the final beers. A novel brewing method assisted by hydrodynamic cavitation was proved able, under suitable process conditions, to retain or generate higher amounts of xanthohumol, desmethylxanthohumol and 6-geranylnaringenin, extending recent evidence about different food and respective bioproducts, as well as adding to its distinct benefits to the ...