The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was ...established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.
The Apicomplexa are obligate intracellular parasites responsible for several important human diseases. These protozoan organisms have evolved several strategies to modify the host cell environment to ...create a favorable niche for their survival. The host cytoskeleton is widely manipulated during all phases of apicomplexan intracellular infection. Moreover, the localization and organization of host organelles are altered in order to scavenge nutrients from the host. Small GTPases are a class of proteins widely involved in intracellular pathways governing different processes, from cytoskeletal and organelle organization to gene transcription and intracellular trafficking. These proteins are already known to be involved in infection by several intracellular pathogens, including viruses, bacteria and protozoan parasites. In this review, we recapitulate the mechanisms by which apicomplexan parasites manipulate the host cell during infection, focusing on the role of host small GTPases. We also discuss the possibility of considering small GTPases as potential targets for the development of novel host-targeted therapies against apicomplexan infections.
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may ...cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
We here report on the existence of Leber's hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, ...affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband's fibroblasts into the cybrid cell model. Finally, all but one of these missense mtDNA variants cluster along the same predicted fourth E-channel deputed to proton translocation within the transmembrane domain of Complex I, involving the ND1, ND4L and ND6 subunits. Hence, the definition of the pathogenic role of a specific mtDNA mutation becomes blurrier than ever and only an accurate evaluation of mitogenome sequence variation data from the general population, combined with functional analyses using the cybrid cell model, may lead to final validation. Our study conclusively shows that even in the absence of a clearly established LHON primary mutation, unprecedented combinations of missense mtDNA variants, individually known as polymorphisms, may lead to reduced OXPHOS efficiency sufficient to trigger LHON. In this context, we introduce a new diagnostic perspective that implies the complete sequence analysis of mitogenomes in LHON as mandatory gold standard diagnostic approach.
Despite over a century of study of malaria parasites, parts of the Plasmodium falciparum life cycle remain virtually unknown. One of these is the early gametocyte stage, a round shaped cell ...morphologically similar to an asexual trophozoite in which major cellular transformations ensure subsequent development of the elongated gametocyte. We developed a protocol to obtain for the first time highly purified preparations of early gametocytes using a transgenic line expressing a green fluorescent protein from the onset of gametocytogenesis. We determined the cellular proteome (1427 proteins) of this parasite stage by high accuracy tandem mass spectrometry and newly determined the proteomes of asexual trophozoites and mature gametocytes, identifying altogether 1090 previously undetected parasite proteins. Quantitative label-free comparative proteomics analysis determined enriched protein clusters for the three parasite developmental stages. Gene set enrichment analysis on the 251 proteins enriched in the early gametocyte proteome revealed that proteins putatively exported and involved in erythrocyte remodeling are the most overrepresented protein set in these stages. One-tenth of the early gametocyte-enriched proteome is constituted of putatively exported proteins, here named PfGEXPs (P. falciparum gametocyte-exported proteins). N-terminal processing and N-acetylation at a conserved leucine residue within the Plasmodium export element pentamotif were detected by mass spectrometry for three such proteins in the early but not in the mature gametocyte sample, further supporting a specific role in protein export in early gametocytogenesis. Previous reports and results of our experiments confirm that the three proteins are indeed exported in the erythrocyte cytoplasm. This work indicates that protein export profoundly marks early sexual differentiation in P. falciparum, probably contributing to host cell remodeling in this phase of the life cycle, and that gametocyte-enriched molecules are recruited to modulate this process in gametocytogenesis.
Malaria long-term elimination depends on parasite transmission control. Plasmodium sexual stage maturation in the mosquito, including egress from the host erythrocyte, is one of the prime targets for ...transmission-blocking interventions. This work aims to identify candidate molecules potentially involved in gamete emergence from the host erythrocyte, as novel transmission blocking targets. We analyzed by quantitative mass spectrometry the proteins released/secreted by purified Plasmodium falciparum gametocytes upon induction of gametogenesis. The proteome obtained showed a good overlap (74%) with the one previously characterized in similar conditions from gametocytes of the rodent malaria parasite P. berghei. Four candidates were selected based on comparative analysis of their abundance values in released vs total gametocyte proteome. We also characterized the P. falciparum orthologue of the microgamete surface protein (MiGS), a marker of male gametocyte secretory vesicles in murine models of malaria. The findings of this study reveal that all the selected candidate proteins are expressed in both genders and localize to vesicle-like structures that respond to gametogenesis stimuli. This result, together with the fact that the selected proteins are released during gamete emergence in both Plasmodium species, makes them interesting candidates for future functional studies to investigate their potential role in the gametogenesis process.
The Mediterranean Sea is a biodiversity hotspot, being home to a vast array of marine species. Furthermore, seawater warming is facilitating the arrival and spread of new thermophilic species, posing ...a severe threat to biodiversity. Among the species currently extending their range and increasing in abundance in Mediterranean waters, sea chubs (genus Kyphosus ) are one of the most enigmatic. One challenge arises from the high phenotypic similarity between the two congeneric species documented in the basin: Kyphosus vaigiensis and Kyphosus sectatrix . Their resemblance has often led to identification challenges, resulting in incorrect or omitted species-level classifications. Therefore, despite the growing presence of these fish in the Mediterranean, it remains unclear whether only one or both species are experiencing a demographic increase and range extension. To date, there have been 26 reports of Kyphosus individuals in the Mediterranean Sea, documented in 24 separate papers. Here, we reviewed the history of the genus in the basin and provided 13 new records of these fish from multiple localities along Mediterranean coasts. In addition, we sequenced the entire mitogenomes of two specimens, assessed their phylogenetic relationships with published Kyphosus mitochondrial DNAs from around the world, and conducted detailed morphological and meristic analyses on one of them, allowing us to provide accurate species-level identifications. Our results indicate that K. vaigiensis is the species currently expanding its range in the Mediterranean Sea, while K. sectatrix is still very rare and only sporadically reported. Notably, our mitogenome data indicate that Mediterranean K. vaigiensis individuals most likely came from Atlantic waters, while there is no evidence to support an entrance through the Red Sea or any other anthropogenic vector. Finally, the potential ecological and fishing impacts associated with the proliferation of these fish in the region are discussed.
Archaeological and genetic evidence concerning the time and mode of wild horse (Equus ferus) domestication is still debated. High levels of genetic diversity in horse mtDNA have been detected when ...analyzing the control region; recurrent mutations, however, tend to blur the structure of the phylogenetic tree. Here, we brought the horse mtDNA phylogeny to the highest level of molecular resolution by analyzing 83 mitochondrial genomes from modern horses across Asia, Europe, the Middle East, and the Americas. Our data reveal 18 major haplogroups (A–R) with radiation times that are mostly confined to the Neolithic and later periods and place the root of the phylogeny corresponding to the Ancestral Mare Mitogenome at ∼130–160 thousand years ago. All haplogroups were detected in modern horses from Asia, but F was only found in E. przewalskii—the only remaining wild horse. Therefore, a wide range of matrilineal lineages from the extinct E. ferus underwent domestication in the Eurasian steppes during the Eneolithic period and were transmitted to modern E. caballus breeds. Importantly, now that the major horse haplogroups have been defined, each with diagnostic mutational motifs (in both the coding and control regions), these haplotypes could be easily used to (i) classify well-preserved ancient remains, (ii) (re)assess the haplogroup variation of modern breeds, including Thoroughbreds, and (iii) evaluate the possible role of mtDNA backgrounds in racehorse performance.
Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor ...secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East.
Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed.
Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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