Transmembrane protein 88: A Wnt regulatory protein that specifies cardiomyocyte development

Genetic regulation of the cell fate transition from lateral plate mesoderm to the specification of cardiomyocytes requires suppression of Wnt/β-catenin signaling, but the mechanism for this is not well understood. By analyzing gene expression and chromatin dynamics during directed differentiation of human embryonic stem cells (hESCs), we identified a suppressor of Wnt/β-catenin signaling, transmembrane protein 88 (TMEM88), as a potential regulator of cardiovascular progenitor cell (CVP) specification. During the transition from mesoderm to the CVP, TMEM88 has a chromatin signature of genes that mediate cell fate decisions, and its expression is highly upregulated in advance of key cardiac transcription factors in vitro and in vivo. In early zebrafish embryos, tmem88a is expressed broadly in the lateral plate mesoderm, including the bilateral heart fields. Short hairpin RNA targeting of TMEM88 during hESC cardiac differentiation increases Wnt/β-catenin signaling, confirming its role as a suppressor of this pathway. TMEM88 knockdown has no effect on NKX2.5 or GATA4 expression, but 80% of genes most highly induced during CVP development have reduced expression, suggesting adoption of a new cell fate. In support of this, analysis of later stage cell differentiation showed that TMEM88 knockdown inhibits cardiomyocyte differentiation and promotes endothelial differentiation. Taken together, TMEM88 is crucial for heart development and acts downstream of GATA factors in the pre-cardiac mesoderm to specify lineage commitment of cardiomyocyte development through inhibition of Wnt/β-catenin signaling

Centrosome-mediated RNA segregation : a novel patterning mechanism in Ilyanassa

Thesis (Ph. D.)--University of Rochester. Dept. of Biology, 2010.All multicellular organisms require asymmetric cell divisions for normal patterning during embryogenesis. Spiralian embryos are thought to be particularly reliant on autonomous cues for embryonic patterning and thus represent potentially useful models for understanding asymmetric cell division. The series of asymmetric divisions that produce the micromere quartets are particularly important for patterning, because they subdivide the animal-vegetal axis into tiers of cells with different developmental potentials. Recently, a novel segregation mechanism has been found in the embryo of the spiralian mud snail Ilyanassa obsoleta: centrosome-mediated RNA segregation. This mechanism results in each quartet inheriting a unique subset of patterning RNAs and has been proposed to be the molecular event responsible for patterning the quartets. In the experiments reported here, I examine how this mode of asymmetric RNA division is established in the Ilyanassa embryo and the development impact of these segregated RNAs. In Chapter 1 I discuss the pertinent background information for this work and discuss the advantages of using Ilyanassa as a model to study RNA segregation. In Chapter 2 I report the work on a conserved patterning gene, Nanos, which was used to develop the tools necessary to do molecular studies in the snail. The major focus of my thesis is discussed in Chapter 3. I show that one of the segregated RNAs, IoLR5, is required in the lineage which inherits it and I characterize two cis-acting elements in localized RNAs, IoLR5 and IoLR1, that mediate transport to the centrosomes. Importantly, these results demonstrate that micromere quartet identity, a hallmark of the ancient spiralian developmental program, is controlled in part by specific RNA localization motifs. I report my attempts to identify trans-acting proteins required for centrosome-mediated RNA segregation in Chapter 4 and summarize my conclusions in Chapter 5

Nanos Is Required in Somatic Blast Cell Lineages in the Posterior of a Mollusk Embryo

SummaryDuring animal development, blast cell lineages are generated by repeated divisions of a mother cell into a series of daughter cells, often with a specific series of distinct fates. Nanos is a translational regulator that is involved in germline development in diverse animals [1–4] and also involved in somatic patterning in insects [5, 6]. Recently, Nanos was found to be required for maintenance of stem cell divisions in the Drosophila germline [7, 8]. We have found that in the mollusk Ilyanassa, Nanos messenger RNA and protein are specifically localized in the mesendodermal blast cell lineage derived from the strongly conserved 4d cell. Nanos activity is required for differentiation of multiple tissues that are derived from the 4d cell, showing that IoNanos is required for somatic development in this embryo. At the cellular level, we show that IoNanos activity is required for the highly stereotyped cleavage pattern of the 4d lineage, the proliferative capacity of the blast cells, and the marked asymmetry of the blast cell divisions. These results suggest that IoNanos is involved in regulating blast cell behaviors in the 4d lineage

An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

Abstract Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids

Detection of X-Ray Polarization from the Blazar 1ES 1959+650 with the Imaging X-Ray Polarimetry Explorer

Observations of linear polarization in the 2–8 keV energy range with the Imaging X-ray Polarimetry Explorer (IXPE) explore the magnetic field geometry and dynamics of the regions generating nonthermal radiation in relativistic jets of blazars. These jets, particularly in blazars whose spectral energy distribution peaks at X-ray energies, emit X-rays via synchrotron radiation from high-energy particles within the jet. IXPE observations of the X-ray-selected BL Lac–type blazar 1ES 1959+650 on 2022 May 3–4 showed a significant linear polarization degree of Π _x = 8.0% ± 2.3% at an electric-vector position angle ψ _x = 123° ± 8°. However, on 2022 June 9–12, only an upper limit of Π _x ≤ 5.1% could be derived (at the 99% confidence level). The degree of optical polarization at that time, Π _O ∼ 5%, is comparable to the X-ray measurement. We investigate possible scenarios for these findings, including temporal and geometrical depolarization effects. Unlike some other X-ray-selected BL Lac objects, there is no significant chromatic dependence of the measured polarization in 1ES 1959+650, and its low X-ray polarization may be attributed to turbulence in the jet flow with dynamical timescales shorter than 1 day

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists