Chronology of the Jafr Prehistory and Protohistory: a Key to the Process of Pastoral Nomadization in the Southern Levant

La question de l’établissement d’une séquence chronologique est primordiale dans le cadre de l’archéologie de la Badia du Levant Sud, afin de permettre de définir une typo-chronologie des différentes structures rencontrées dans les périphéries désertiques. Les sites du Bassin d’al-Jafr, dans le sud de la Jordanie, permettent d’apporter des éléments de réponse significatifs sur cette question. Les recherches effectuées dans cette région ont montré que l’occupation post-pléistocène a commencé au cours du PPNB par le développement d’établissements agro-pastoraux dans le Wadi Abu Tulayha et à Wadi Ghuweir 17, suivi par la première Phase d’occupation pastorale nomade dans ce secteur, représentée par les nécropoles ou les sanctuaires ouverts du PPNC/Néolithique récent à Harra al-Juhayra et Qa’ Abu Tulayha West. Ce processus a abouti à la mise en place de sociétés véritablement nomades de l’âge du Bronze ancien, attestées par les champs de cairns funéraires du Wadi Burma et Tal’at ’Ubayda. À travers une synthèse de ces données issues des recherches entreprises dans le Bassin d’al-Jafr, une séquence chronologique de l’occupation pastorale préhistorique et protohistorique de ce secteur est proposée à titre provisoire dans cet article, permettant d’aborder la question du processus de développement du phénomène pastoral nomade à une échelle géographique plus large.The top-priority issue of the Badia archaeology in the southern Levant is to establish a chronological framework for seriating various features dotted in arid peripheries. The Jafr Basin sites in southern Jordan provide insights into the issue. A series of investigations has shown that the post-Pleistocene land use history of the arid basin began with the short-range pastoral transhumance evidenced at the PPNB agro-pastoral outposts of Wadi Abu Tulayha and Wadi Ghuwayr 17, through the initial pastoral nomadism suggested at the PPNC/LN isolated cemeteries or open sanctuaries of Harrat al-Juhayra and Qa’Abu Tulayha West, and then came to the establishment of full-fledged nomadic society represented by the EBA large-scale cairn fields of Wadi Burma and Tal’at ’Ubayda. Reviewing the previous investigation results, this paper presents a tentative chronology of the Jafr pastoral prehistory and protohistory and, on this base, briefly discusses the process of pastoral nomadization in the basin and its surrounding areas.يعتبر إنشاء إطار زمني للعديد من المعالم الموجودة في الأطراف الجنوبية الجافة لبادية الشام من أهم القضايا لعلم الآثار. وتقدم مواقع حوض الجفر في جنوب الأردن نظرة متعمقة في هذا الشأن. وقد أظهرت سلسلة من التحقيقات في تاريخ أستخدام الأرض الجافة في فترة ما بعد البلايستوسين أن هذا الإستخدام بدأ من خلال البداوة القصيرة المدى كما تشير الأدلة من مواقع وداي أبو طليحة ووادي الغوير 17 والتي ترجع الى البؤرة الإستيطانية الزراعيةذالبدوية من فترة العصر الحجري الحديث ما قبل الفخاري الفترة ب, وكذلك خلال الفترة المتأخرة من العصر الحجري الحديث ما قبل الفخاري والعصر الحجري الحديث الفخاري كما هو الحال في المقابر المنعزلة في حرة الجهيرة وقاع أبو طليحة الغربي‪,‬ وحتى ظهور مجتمع البدواة الكاملة في العصر البرونزي المبكر كما هو الحال في الرجوم الكثيرة في موقع وادي البرما وتلعة عبيدة. واستناداً الى نتائج التحقيقات السابقة تقدم هذه الورقة محاولة لوضع تسلسل زمني للبدواة في منطقة الجفر خلال عصور ما قبل التاريخ وبداية العصور البرونزية وكذلك تناقش عملية البداوة في منطقة الجفر والمناطق المحيطة

Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation

<p>Abstract</p> <p>Background</p> <p>In the silkworm, <it>Bombyx mori</it>, femaleness is strongly controlled by the female-specific W chromosome. Originally, it was presumed that the W chromosome encodes female-determining gene(s), accordingly called <it>Fem</it>. However, to date, neither <it>Fem </it>nor any protein-coding gene has been identified from the W chromosome. Instead, the W chromosome is occupied with numerous transposon-related sequences. Interestingly, the silkworm W chromosome is a source of female-enriched PIWI-interacting RNAs (piRNAs). piRNAs are small RNAs of 23-30 nucleotides in length, which are required for controlling transposon activity in animal gonads. A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet.</p> <p>Results</p> <p>Here we molecularly characterize the KG line. Genomic PCR analyses using currently available W chromosome-specific PCR markers indicated that no large deletion existed in the KG W chromosome. Genetic analyses demonstrated that sib-crosses within the KG line suppressed masculinization. Masculinization reactivated when crossing KG females with wild type males. Importantly, the KG ovaries exhibited a significantly abnormal transcriptome. First, the KG ovaries misexpressed testis-specific genes. Second, a set of female-enriched piRNAs was downregulated in the KG ovaries. Third, several transposons were overexpressed in the KG ovaries.</p> <p>Conclusions</p> <p>Collectively, the mutation in the KG W chromosome causes broadly altered expression of testis-specific genes, piRNAs, and transposons. To our knowledge, this is the first study that describes a W chromosome mutant with such an intriguing phenotype.</p

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology