Biodiversity and physiological characteristics of Antarctic and Arctic lichens-associated bacteria

The diversity and physiological characteristics of culturable bacteria associated with lichens from different habitats of the Arctic and Antarctica were investigated. The 68 retrieved isolates could be grouped on the basis of their 16S rRNA gene sequences into 26 phylotypes affiliated with the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes and with the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Isolates belonging to the Alphaproteobacteria were the most abundant, followed by those belonging to Actinobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus. Phylogenetic analysis showed that approximately 21 % of the total isolates represented a potentially novel species or genus (≤97 % sequence similarity). Strains belonging to the genera Sphingomonas, Frondihabitans, Hymenobacter, and Burkholderia were recovered from lichen samples from both geographic locations, implying common and important bacterial functions within lichens. Extracellular protease activities were detected in six isolates, affiliated with Burkholderia, Frondihabitans, Hymenobacter, Pseudomonas, and Rhodanobacter. Extracellular lipase activities were detected in 37 isolates of the genera Burkholderia, Deinococcus, Frondihabitans, Pseudomonas, Rhodanobacter, Sphingomonas, and Subtercola. This is the first report on the culturable bacterial diversity present within lichens from Arctic and Antarctica and the isolates described herein are valuable resources to decode the functional and ecological roles of bacteria within lichens. In addition, the low similarity (≤97 %) of the recovered isolates to known species and their production of cold-active enzymes together suggest that lichens are noteworthy sources of novel bacterial strains for use in biotechnological applications.     

Cell Fate Decisions in Malignant Hematopoiesis: Leukemia Phenotype Is Determined by Distinct Functional Domains of the MN1 Oncogene

Extensive molecular profiling of leukemias and preleukemic diseases has revealed that distinct clinical entities, like acute myeloid (AML) and T-lymphoblastic leukemia (T-ALL), share similar pathogenetic mutations. It is not well understood how the cell of origin, accompanying mutations, extracellular signals or structural differences in a mutated gene determine the phenotypic identity of leukemias. We dissected the functional aspects of different protein regions of the MN1 oncogene and their effect on the leukemic phenotype, building on the ability of MN1 to induce leukemia without accompanying mutations. We found that the most C-terminal region of MN1 was required to block myeloid differentiation at an early stage, and deletion of an extended C-terminal region resulted in loss of myeloid identity and cell differentiation along the T-cell lineage in vivo. Megakaryocytic/erythroid lineage differentiation was blocked by the N-terminal region. In addition, the N-terminus was required for proliferation and leukemogenesis in vitro and in vivo through upregulation of HoxA9, HoxA10 and Meis2. Our results provide evidence that a single oncogene can modulate cellular identity of leukemic cells based on its active gene regions. It is therefore likely that different mutations in the same oncogene may impact cell fate decisions and phenotypic appearance of malignant diseases.     

Tertiary-Amine Functionalized Polyplexes Enhanced Cellular Uptake and Prolonged Gene Expression

Ultrasound (US) has been found to facilitate the transport of DNA across cell membranes. However, the transfection efficiency is generally low, and the expression duration of the transfected gene is brief. In this study, a tertiary polycation, Poly(2-(dimethylamino) ethyl methacrylate) (PDMAEMA), was used as a carrier for US-mediated gene transfection. Its in-vitro and in-vivo effects on the transfection efficiency and the expression duration were evaluated. A mixture of pCI-neo-luc and PDMAEMA was transfected to cultured cells or mouse muscle by exposure to 1-MHz pulse US. A strong expression of luciferase was found 10 days after the transfection in vitro regardless of US exposure. However, effective transfection only occurred in the US groups in vivo. The transfection ability depended on the weight ratio of PDMAEMA to DNA, and was different for the in-vitro and in-vivo conditions. Lower weight ratios, e.g., 0.25, exhibited better in-vivo expression for at least 45 days.     

Statistical analysis of data from limiting dilution cloning to assess monoclonality in generating manufacturing cell lines

Assurance of monoclonality of recombinant cell lines is a critical issue to gain regulatory approval in biological license application (BLA). Some of the requirements of regulatory agencies are the use of proper documentations and appropriate statistical analysis to demonstrate monoclonality. In some cases, one round may be sufficient to demonstrate monoclonality. In this article, we propose the use of confidence intervals for assessing monoclonality for limiting dilution cloning in the generation of recombinant manufacturing cell lines based on a single round. The use of confidence intervals instead of point estimates allow practitioners to account for the uncertainty present in the data when assessing whether an estimated level of monoclonality is consistent with regulatory requirements. In other cases, one round may not be sufficient and two consecutive rounds are required to assess monoclonality. When two consecutive subclonings are required, we improved the present methodology by reducing the infinite series proposed by Coller and Coller (Hybridoma 1983;2:91–96) to a simpler series. The proposed simpler series provides more accurate and reliable results. It also reduces the level of computation and can be easily implemented in any spreadsheet program like Microsoft Excel. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1061–1068, 2016     

Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix

A Gram-negative, strictly aerobic, non-motile, rod-shaped and psychrophilic bacterial strain, PAMC 27137^T, was isolated from the marine sediment of the Ross Sea, Antarctica. Strain PAMC 27137^T was observed to grow at 4–10 °C, at pH 6.5–7.5 and in the presence of 2.5–4.0 % (w/v) sea salts. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain PAMC 27137^T belongs to the genus Lacinutrix showing the high similarities with Lacinutrix mariniflava JCM 13824^T (97.6 %) and Lacinutrix algicola JCM 13825^T (97.1 %). Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 27137^T is clearly distinguished from the most closely related Lacinutrix species. The major fatty acids (>5 %) were identified as iso-C_15:1 G (19.9 %), iso-C_15:0 (19.3 %), iso-C_17:0 3-OH (11.3 %), summed feature 9 (C_16:0 10-methyl and/or iso-C_17:1 ω9c as defined by MIDI, 9.1 %), iso-C_15:0 3-OH (7.5 %), and anteiso-C_15:1 A (5.8 %). The polar lipids were found to consist of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and five unidentified phospholipids. The major respiratory quinone was identified as MK-6. The genomic DNA G+C content was determined to be 32.1 mol%. Based on the data from this polyphasic taxonomic study, strain PAMC 27137^T is considered to represent a novel species of the genus Lacinutrix, for which the name Lacinutrix jangbogonensis sp. nov. is proposed. The type strain is PAMC 27137^T (=KCTC 32573^T=JCM 19883^T).     

The cytoprotective role of autophagy in puromycin aminonucleoside treated human podocytes

Autophagy is a ubiquitous catabolic process involving degradation of damaged organelles and protein aggregates. It shows cytoprotective effects in many cell types and helps to maintain cell homeostasis. In many glomerular diseases, podocyte damage leads to the disruption of the renal filtration barrier and subsequent proteinuria. Puromycin aminonucleoside (PAN) which induces podocyte apoptosis in vitro and in vivo is widely used for studying the pathophysiology of glomerular diseases. It has been shown that PAN induces autophagy in podocytes. However, the relationship between autophagy and apoptosis in PAN treated human podocytes is not known and the role of PAN-induced autophagy in podocyte survival remains unclear. Here we demonstrate that PAN induced autophagy in human podocytes prior to apoptosis which was featured with the activation of mTOR complex 1 (mTORC1). When the PAN-induced autophagy was inhibited by 3-methyladenine (3-MA) or chloroquine (CQ), podocyte apoptosis increased significantly along with the elevation of active caspase-3. Under such circumstance, the podocyte cytoskeleton was also disrupted. Collectively, our results suggested that the induced autophagy may be an early adaptive cytoprotective mechanism for podocyte survival after PAN treatment.     

Counteracting apoptosis and necrosis with hypoxia responsive expression of Bcl-2Delta

In the encapsulated environment of biohybrid artificial organs, cells often encounter a deficiency in oxygen, which lead to apoptosis, necrosis, and lost of productivity. Two vectors with constitutive CMV promoters were constructed to examine the ability of Bcl-2Delta to help C2C12 mouse myoblasts maintain exogenous protein production under hypoxia. Two additional vectors with hypoxia-inducible promoters (5HRE) that switched on Bcl-2Delta expression based on low oxygen levels (0.0%, 0.5%, 1.0%, 2.0%, 5.0%, or 21.0%) were tested for protein productivity and protection against hypoxic stresses. A yellow fluorescent protein was used as a model protein in all vector constructs. C2C12 cells with Bcl-2Delta consistently produced more protein regardless of the oxygen level or promoter used. Cells utilizing the 5HRE rather than the CMV promoter showed an increased level of protein production as the oxygen was decreased. Among the cells with 5HRE promoters, the presence of Bcl-2Delta also increased viability and decreased apoptosis.     

Searching cell-secreted proteomes for potential urinary bladder tumor markers

To search for biomarkers critical for bladder carcinoma diagnosis and prognosis, secreted proteomes of highly malignant U1 and pre-malignant U4 cell lines were initially analyzed. Proteins in the culture media of the U1 and U4 cell lines were systematically examined by SDS-PAGE combined with MALDI-TOF MS. Among them, expression of pro-u-plasminogen activator (pro-u-PA) was confirmed by Western blot analysis and further evaluated. In analyzing urine samples from bladder cancer patients and normal subjects, we established a statistically significant relationship between the low level and absence of pro-u-PA in urine with high stages and grades of the tumor samples. Constitutive expression of Ras dominant negative protein led to increased expression of pro-u-PA in culture media, indicating that the loss of pro-u-PA is associated with oncogenic transformation. Analysis of cancer-secreted proteomes can be a feasible, non-invasive and efficient strategy for searching potential bladder tumor biomarkers. Our work also has identified the loss of pro-u-PA in urine as potential marker of more advanced bladder carcinoma.