scholarly journals Contamination detection in sequencing studies using the mitochondrial phylogeny

2021 ◽  
Vol 31 (2) ◽  
pp. 309-316
Author(s):  
Hansi Weissensteiner ◽  
Lukas Forer ◽  
Liane Fendt ◽  
Azin Kheirkhah ◽  
Antonio Salas ◽  
...  
Keyword(s):  
Sequencing Studies ◽  
Mitochondrial Phylogeny

Clinical features and operative technique of transinfundibular craniopharyngioma

2020 ◽  
Vol 133 (1) ◽  
pp. 119-128 ◽  
Author(s):  
Bin Tang ◽  
ShenHao Xie ◽  
GuanLin Huang ◽  
ZhiGang Wang ◽  
Le Yang ◽  
...  
Keyword(s):  
Clinical Features ◽  
Operative Technique ◽  
Third Ventricle ◽  
Radical Resection ◽  
The Third ◽  
Expanded Endonasal Approach ◽  
Sequencing Studies ◽  
Characteristic Features ◽  
Mri Study ◽  
Adamantinomatous Craniopharyngioma

OBJECTIVETransinfundibular craniopharyngioma (TC) is one of the 4 subtypes of suprasellar craniopharyngioma. In this study, the authors analyzed the clinical features of and operative technique for TC.METHODSA total of 95 consecutive cases of suprasellar craniopharyngioma that had been resected via the endoscopic expanded endonasal approach were retrospectively reviewed. Patients were divided into 2 groups: 34 in the TC group and 61 in the nontransinfundibular craniopharyngioma (NC) group. Clinical and radiographic features, intraoperative findings, histopathological and genetic findings, and surgical outcomes were analyzed and compared between groups.RESULTSCompared with NC, TC was mostly seen in adult patients (97.1%); it was rare in children (2.9%). Clinical presentations tended toward headache, hydrocephalus, and diabetes insipidus. The relatively smaller volume, midline location (consistent with the stalk position), unidentifiable stalk, no shift of the third ventricle, and greater likelihood to involve the third ventricle and cause hydrocephalus were the characteristic features of TC in the preoperative MRI study. According to the degree of vertical extension of the tumor, the 34 TCs could be classified into 3 subtypes: type 1, entity was limited to stalk (n = 2, 5.9%); type 2, tumor extended up to the third ventricle (type 2a) or down to the subdiaphragmatic cavity (type 2b) (n = 23, 67.6%); and type 3, tumor extended in both directions (n = 9, 26.5%). For TC resection, the chiasm–pituitary corridor, lamina terminalis corridor, and pituitary corridor could be used separately or jointly. Most of the TCs originated from the infundibulum–tuber cinereum, grew within and along the long axis of the infundibulum, and the pituitary stalk was not usually preserved in TCs (20.6%), whereas the rate of preservation was higher (80.3%) in NCs. Bilateral hypothalamic injury was found in nearly all TCs if radical resection was performed, whereas the relationship between NCs and hypothalamus was either compression (32.8%) or unilateral invasion (67.2%). Meanwhile, the postoperative endocrine and neuropsychological function outcomes in patients with TC were worse than in patients with NC. The genetic analysis with whole-exome sequencing studies showed no differential mutations of CTNNB1 (β-catenin) and BRAF (V600E) between TC and NC subtypes, but there was a difference between adamantinomatous craniopharyngioma and papillary craniopharyngioma.CONCLUSIONSTC is a special subtype of suprasellar craniopharyngioma, which is remarkably different from NC. Identification of this type of tumor preoperatively is essential for the planning of appropriate surgical approach and degree of excision.

scholarly journals Human dermal fibroblast subpopulations are conserved across single-cell RNA sequencing studies

2020 ◽  
Author(s):  
Alex M. Ascensión ◽  
Sandra Fuertes-Álvarez ◽  
Olga Ibañez-Solé ◽  
Ander Izeta ◽  
Marcos J. Araúzo-Bravo
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Dermal Fibroblast ◽  
Human Dermal Fibroblast ◽  
Single Cell Rna Sequencing ◽  
Sequencing Studies

scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

scholarly journals Bantu-speaker migration and admixture in southern Africa

2020 ◽  
Author(s):  
Ananyo Choudhury ◽  
Dhriti Sengupta ◽  
Michele Ramsay ◽  
Carina Schlebusch
Keyword(s):  
Southern Africa ◽  
Geographic Region ◽  
Middle Stone Age ◽  
East African ◽  
Variant Discovery ◽  
African Populations ◽  
Sequencing Studies ◽  
Anatomically Modern Humans ◽  
Scale Population ◽  
Novel Variant

Abstract The presence of Early and Middle Stone Age human remains and associated archaeological artefacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa have largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies hinting at the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.

scholarly journals A Novel Mutation in Cse1l Disrupts Brain and Eye Development with Specific Effects on Pax6 Expression

2021 ◽  
Vol 9 (3) ◽  
pp. 27
Author(s):  
Lauren E. Blizzard ◽  
Chelsea Menke ◽  
Shaili D. Patel ◽  
Ronald R. Waclaw ◽  
Salil A. Lachke ◽  
...  
Keyword(s):  
Neural Development ◽  
Null Allele ◽  
Eye Development ◽  
Novel Mutation ◽  
Forward Genetics ◽  
Mammalian Development ◽  
Variants Of Unknown Significance ◽  
New Genes ◽  
Conditional Allele ◽  
Sequencing Studies

Forward genetics in the mouse continues to be a useful and unbiased approach to identifying new genes and alleles with previously unappreciated roles in mammalian development and disease. Here, we report a new mouse allele of Cse1l that was recovered from an ENU mutagenesis screen. Embryos homozygous for the anteater allele of Cse1l display a number of variable phenotypes, with craniofacial and ocular malformations being the most obvious. We provide evidence that Cse1l is the causal gene through complementation with a novel null allele of Cse1l generated by CRISPR-Cas9 editing. While the variability in the anteater phenotype was high enough to preclude a detailed molecular analysis, we demonstrate a very penetrant reduction in Pax6 levels in the developing eye along with significant ocular developmental phenotypes. The eye gene discovery tool iSyTE shows Cse1l to be significantly expressed in the lens from early eye development stages in embryos through adulthood. Cse1l has not previously been shown to be required for organogenesis as homozygosity for a null allele results in very early lethality. Future detailed studies of Cse1l function in craniofacial and neural development will be best served with a conditional allele to circumvent the variable phenotypes we report here. We suggest that human next-generation (whole genome or exome) sequencing studies yielding variants of unknown significance in CSE1L could consider these findings as part of variant analysis.

scholarly journals Mitochondrial phylogeny of the deep-sea squat lobsters, Munidopsidae (Galatheoidea)

2011 ◽  
Vol 250 (4) ◽  
pp. 367-377 ◽  
Author(s):  
Shane T. Ahyong ◽  
Nikos Andreakis ◽  
Joanne Taylor
Keyword(s):  
Deep Sea ◽  
Mitochondrial Phylogeny ◽  
Squat Lobsters
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