MicroRNAs in early embryonic development : dissecting the role of miR-290 through miR-295 in the mouse

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.Includes bibliographical references.MicroRNAs mediate developmental regulation of gene expression via translational repression of target mRNAs. Targeted deletion of the miRNA biogenesis machinery in the mouse has demonstrated essential roles for miRNAs during early development. In this thesis, I have examined the role of a family of miRNAs, miR-290 through miR-295 (miR-290 cluster), which are specifically expressed during early embryonic and germ cell development. This miRNA family is conserved only among mammals. miR-290 cluster miRNAs are transcribed and processed from a common capped and polyadenylated primary transcript in the mouse. Deletion of the miR-290 cluster in the mouse results in early embryonic lethality and misregulation of primordial germ cell migration, ultimately resulting in germ cell depletion, premature ovarian failure and infertility in the adult female. Loss of miR-290-295 mediated repression results in significant changes in the gene expression profile of embryonic stem cells, allowing for the accumulation and precocious expression of many developmental regulators involved in differentiation. As such, we have shown that the miR-290 cluster miRNAs are critical regulators of embryonic development.by Lucas M. Dennis.Ph.D

Widest geographic distribution of a shallow and mesophotic antipatharian coral (Anthozoa: Hexacorallia): Antipathes grandis VERRILL, 1928 – confirmed by morphometric and molecular analyses

We provide the first record of the shallow and mesophotic ( 200 m depth) benthic taxa have such wide geographic distributions

Reversible Switching of Spiropyran Molecules in Direct Contact With a Bi(111) Single Crystal Surface

Photochromic molecular switches immobilized by direct contact with surfaces typically show only weak response to optical excitation, which often is not reversible. In contrast, here, it is shown that a complete and reversible ring-opening and ring-closing reaction of submonolayers of spironaphthopyran on the Bi(111) surface is possible. The ring opening to the merocyanine isomer is initiated by ultraviolet light. Switching occurs in a two-step process, in which after optical excitation, an energy barrier needs to be overcome to convert to the merocyanine form. This leads to a strong temperature dependence of the conversion efficiency. Switching of the merocyanine isomer back to the closed form is achieved by a temperature increase. Thus, the process can be repeated in a fully reversible manner, in contrast to previously studied nitrospiropyran molecules on surfaces. This is attributed to the destabilization of the merocyanine isomer by the electron-donating nature of the naphtho group and the reduced van der Waals interaction of the Bi(111) surface. The result shows that molecules designed for switching in solutions need to be modified to function in direct contact with a surface

Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.Peer reviewe

What, if anything, is Quaternary?

The formal recognition of Quaternary as a Period/ System was approved by IUGS in June 2009, in accordance with a proposal originated by INQUA. There are reasons to believe that this will have destabilizing consequences for the geological time scale. Until now, the primary divisions of the stratigraphic record, at the Period level and above, have been based on the progressive change of Earth’s biota. The Quaternary, on the other hand, is a paleoclimatic concept based on glacial-interglacial variability, expressed in lithological change. The IUGS vote holds that this paradigm now supersedes the biochronological identity of the Neogene Period/System. Furthermore, to accommodate the most recent INQUA opinion about “when the Ice Ages began”, the ICS agreed to relocate the base of the Pleistocene to 2.59 Ma from 1.81 Ma, enlarging the epoch by 43% and again without regard for its original paleontological definition, or for the vast literature in other fields of Pleistocene research. If history is a guide, the resulting disruption in late Cenozoic marine and vertebrate paleontology, human evolution, paleoceanography and paleoclimatology will be widely resisted, with potential impact on the authority of IUGS. The consequence of abandoning basic principles in order to satisfy the interest of a special group deserves a wider consideration than it has so far received

Diagnostic Performance of convolutional neural networks for dental sexual dimorphism

Convolutional neural networks (CNN) led to important solutions in the field of Computer Vision. More recently, forensic sciences benefited from the resources of artificial intelligence, especially in procedures that normally require operator-dependent steps. Forensic tools for sexual dimorphism based on morphological dental traits are available but have limited performance. This study aimed to test the application of a machine learning setup to distinguish females and males using dentomaxillofacial features from a radiographic dataset. The sample consisted of panoramic radiographs (n = 4003) of individuals in the age interval of 6 and 22.9 years. Image annotation was performed with V7 software (V7labs, London, UK). From Scratch (FS) and Transfer Learning (TL) CNN architectures were compared, and diagnostic accuracy tests were used. TL (82%) performed better than FS (71%). The correct classifications of females and males aged ≥ 15 years were 87% and 84%, respectively. For females and males < 15 years, the correct classifications were 80% and 83%, respectively. The Area Under the Curve (AUC) from Receiver-operating Characteristic (ROC) curves showed high classification accuracy between 0.87 and 0.91. The radio-diagnostic use of CNN for sexual dimorphism showed positive outcomes and promising forensic applications to the field of dental human identification

Cerebellar c9RAN proteins associate with clinical and neuropathological characteristics of C9ORF72 repeat expansion carriers.

Clinical and neuropathological characteristics associated with G4C2 repeat expansions in chromosome 9 open reading frame 72 (C9ORF72), the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, are highly variable. To gain insight on the molecular basis for the heterogeneity among C9ORF72 mutation carriers, we evaluated associations between features of disease and levels of two abundantly expressed "c9RAN proteins" produced by repeat-associated non-ATG (RAN) translation of the expanded repeat. For these studies, we took a departure from traditional immunohistochemical approaches and instead employed immunoassays to quantitatively measure poly(GP) and poly(GA) levels in cerebellum, frontal cortex, motor cortex, and/or hippocampus from 55 C9ORF72 mutation carriers [12 patients with ALS, 24 with frontotemporal lobar degeneration (FTLD) and 19 with FTLD with motor neuron disease (FTLD-MND)]. We additionally investigated associations between levels of poly(GP) or poly(GA) and cognitive impairment in 15 C9ORF72 ALS patients for whom neuropsychological data were available. Among the neuroanatomical regions investigated, poly(GP) levels were highest in the cerebellum. In this same region, associations between poly(GP) and both neuropathological and clinical features were detected. Specifically, cerebellar poly(GP) levels were significantly lower in patients with ALS compared to patients with FTLD or FTLD-MND. Furthermore, cerebellar poly(GP) associated with cognitive score in our cohort of 15 patients. In the cerebellum, poly(GA) levels similarly trended lower in the ALS subgroup compared to FTLD or FTLD-MND subgroups, but no association between cerebellar poly(GA) and cognitive score was detected. Both cerebellar poly(GP) and poly(GA) associated with C9ORF72 variant 3 mRNA expression, but not variant 1 expression, repeat size, disease onset, or survival after onset. Overall, these data indicate that cerebellar abnormalities, as evidenced by poly(GP) accumulation, associate with neuropathological and clinical phenotypes, in particular cognitive impairment, of C9ORF72 mutation carriers

Nuclear rupture at sites of high curvature compromises retention of DNA repair factors.

The nucleus is physically linked to the cytoskeleton, adhesions, and extracellular matrix-all of which sustain forces, but their relationships to DNA damage are obscure. We show that nuclear rupture with cytoplasmic mislocalization of multiple DNA repair factors correlates with high nuclear curvature imposed by an external probe or by cell attachment to either aligned collagen fibers or stiff matrix. Mislocalization is greatly enhanced by lamin A depletion, requires hours for nuclear reentry, and correlates with an increase in pan-nucleoplasmic foci of the DNA damage marker γH2AX. Excess DNA damage is rescued in ruptured nuclei by cooverexpression of multiple DNA repair factors as well as by soft matrix or inhibition of actomyosin tension. Increased contractility has the opposite effect, and stiff tumors with low lamin A indeed exhibit increased nuclear curvature, more frequent nuclear rupture, and excess DNA damage. Additional stresses likely play a role, but the data suggest high curvature promotes nuclear rupture, which compromises retention of DNA repair factors and favors sustained damage