bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial fission and fusion in Dictyostelium discoideum: a search for proteins involved in membrane dynamics
Authors: Schimmel Brixey G , Berbusse Gregory W , Naylor Kari 
Published: September 2012

Abstract

Background
Mitochondrial morphology is maintained by two distinct membrane events -fission and fusion. Altering these conserved processes can disrupt mitochondrial morphology and distribution, thereby disrupting the organelle’s functionality and impeding cellular function. In higher eukaryotes, these processes are mediated by a family of dynamin-related proteins (DRP’s). In the lower eukaryotes, for instance Dictyostelium discoideum, mitochondrial fission and fusion have been implicated but not yet established. To understand the overall mechanism of these dynamics across organisms, we developed an assay to identify fission and fusion events in Dictyostelium and to assess the involvement of the mitochondrial proteins, MidA, CluA, and two DRP’s, DymA and DymB.

Findings
Using laser scanning confocal microscopy we show, for the first time, that lower eukaryotes mediate mitochondrial fission and fusion. In Dictyostelium, these processes are balanced, occurring approximately 1 event/minute. Quantification of the rates in midA
-, cluA
-, dymA

-
, or dymB

-
strains established that MidA appears to play an indirect role in the regulation of fission and fusion, while the DRP’s are not essential for these processes. Rates of fission and fusion were significantly reduced in cluA
-cells, indicating that CluA is necessary for maintaining both fission and fusion.

Conclusions
We have successfully demonstrated that Dictyostelium mitochondria undergo the dynamic processes of fission and fusion. The classical mediators of membrane dynamics - the DRP’s – are not necessary for these dynamics, whereas CluA is necessary for both processes. This work contributes to our overall understanding of mitochondrial dynamics and ultimately will provide additional insight into mitochondrial disease.
Identification of suitable endogenous control genes for microRNA expression profiling of childhood medulloblastoma and human neural stem cells
Authors: Genovesi Laura A , Anderson Denise , Carter Kim W , Giles Keith M , Dallas Peter B 
Published: September 2012

AbstractBackgroundMedulloblastoma (MB) is the most common type of malignant childhood brain tumour. Although deregulated microRNA (miRNA) expression has been linked to MB pathogenesis, the selection of appropriate candidate endogenous control (EC) reference genes for MB miRNA expression profiling studies has not been systematically addressed. In this study we utilised reverse transcriptase quantitative PCR (RT-qPCR) to identify the most appropriate EC reference genes for the accurate normalisation of miRNA expression data in primary human MB specimens and neural stem cells.ResultsExpression profiling of 662 miRNAs and six small nuclear/ nucleolar RNAs in primary human MB specimens, two CD133+ neural stem cell (NSC) populations and two CD133- neural progenitor cell (NPC) populations was performed using TaqMan low-density array (TLDA) cards. Minimal intra-card variability for candidate EC reference gene replicates was observed, however significant inter-card variability was identified between replicates present on both TLDA cards A and B. A panel of 18 potentially suitable EC reference genes was identified for the normalisation of miRNA expression on TLDA cards. These candidates were not significantly differentially expressed between CD133+ NSCs/ CD133- NPCs and primary MB specimens. Of the six sn/snoRNA EC reference genes recommended by the manufacturer, only RNU44 was uniformly expressed between primary MB specimens and CD133+ NSC/CD133- NPC populations (P = 0.709; FC = 1.02). The suitability of candidate EC reference genes was assessed using geNorm and NormFinder software, with hsa-miR-301a and hsa-miR-339-5p found to be the most uniformly expressed EC reference genes on TLDA card A and hsa-miR-425* and RNU24 for TLDA card B.ConclusionsA panel of 18 potential EC reference genes that were not significantly differentially expressed between CD133+ NSCs/ CD133- NPCs and primary human MB specimens was identified. The top ranked EC reference genes described here should be validated in a larger cohort of specimens to verify their utility as controls for the normalisation of RT-qPCR data generated in MB miRNA expression studies. Importantly, inter-card variability observed between replicates of certain candidate EC reference genes has major implications for the accurate normalisation of miRNA expression data obtained using the miRNA TLDA platform.
Dysfunctional telomeres in primary cells from Fanconi anemia FANCD2 patients
Authors: Joksic Ivana , Vujic Dragana , Guc-Scekic Marija , Leskovac Andreja , Petrovic Sandra , Ojani Maryam , Trujillo Juan P , Surralles Jordi , Zivkovic Maja , Stankovic Aleksandra , Slijepcevic Predrag , Joksic Gordana 
Published: September 2012

Background
Fanconi anemia (FA) is characterized by sensitivity to DNA cross-linking agents, mild cellular, and marked clinical radio sensitivity. In this study we investigated telomeric abnormalities of non-immortalized primary cells (lymphocytes and fibroblasts) derived from FA patients of the FA-D2 complementation group, which provides a more accurate physiological assessment than is possible with transformed cells or animal models.

Results
We analyzed telomere length, telomere dysfunction-induced foci (TIFs), sister chromatid exchanges (SCE), telomere sister chromatid exchanges (T-SCE), apoptosis and expression of shelterin components TRF1 and TRF2. FANCD2 lymphocytes exhibited multiple types of telomeric abnormalities, including premature telomere shortening, increase in telomeric recombination and aberrant telomeric structures ranging from fragile to long-string extended telomeres. The baseline incidence of SCE in FANCD2 lymphocytes was reduced when compared to control, but in response to diepoxybutane (DEB) the 2-fold higher rate of SCE was observed. In contrast, control lymphocytes showed decreased SCE incidence in response to DEB treatment. FANCD2 fibroblasts revealed a high percentage of TIFs, decreased expression of TRF1 and invariable expression of TRF2. The percentage of TIFs inversely correlated with telomere length, emphasizing that telomere shortening is the major reason for the loss of telomere capping function. Upon irradiation, a significant decrease of TIFs was observed at all recovery times. Surprisingly, a considerable percentage of TIF positive cells disappeared at the same time when incidence of γ-H2AX foci was maximal. Both FANCD2 leucocytes and fibroblasts appeared to die spontaneously at higher rate than control. This trend was more evident upon irradiation; the percentage of leucocytes underwent apoptosis was 2.59- fold higher than that in control, while fibroblasts exhibited a 2- h delay before entering apoptosis.

Conclusion
The results of our study showed that primary cells originating from FA-D2 patients display shorten telomeres, elevated incidence of T-SCEs and high frequency of TIFs. Disappearance of TIFs in early response to irradiation represent distinctive feature of FANCD2 cells that should be examined further.
Effect of adiponectin gene polymorphisms on waist circumference in patients with diabetes
Authors: Hasani-Ranjbar Shirin , Amoli Mahsa M , Tabatabaei-Malazy Ozra , Rumi Yalda , Tavakkoly-Bazzaz Javad , Samimi Hilda , Abbasifarid Elnaz 
Published: September 2012

Abstract
Background
Plasma levels of adiponectin which is secreted from adipose tissue are associated with various parameters of metabolic syndrome. This effect seems to be a result of interactions between genetic and environmental factors including central obesity. The present study was carried out to investigate the possibility of relation between single nucleotide polymorphisms of adiponectin gene (+45 T/G and −11391 G/A) and waist circumferences (WC) in patients with type 2 diabetes.

Methods
This cross-sectional study was conducted on n = 238 diabetic patients selected as cases and n = 159 as healthy control who were recruited from Rafsanjan city in south – east of Iran. The possible association of +45 T/G and –11391 G/A adiponectin gene polymorphisms with WC according to age and sex was evaluated.

Results
There was no significant difference in distribution of frequencies of +45 T/G and –11391 G/A adiponectin gene polymorphisms in each group. We only found a significant association between –11391 G/A adiponectin gene polymorphism with WC in diabetic group (p = 0.021). This association was remained significant after adjustment in multivariate regression model (p = 0.019, OR: 0.244, 95%CI: 0.075-0.791) and also this effect was independent of sex and age.

Conclusion
We found higher abdominal obesity in GA or AA carriers of adiponectin – 11391 G/A genotype in type 2 diabetes patients independent of age and sex.
Identification of a Signaling Axis HIF-1α/MicroRNA-210/ISCU Independent of SDH Mutation That Defines a Subgroup of Head and Neck Paragangliomas
Authors: Merlo Anna , de Quiros Sandra Bernaldo , Secades Pablo , Zambrano Iriana , Balbín Milagros , Astudillo Aurora , Scola Bartolomé , Arístegui Miguel , Suarez Carlos , Chiara María-Dolores 
Published: September 2012

Background:
Head and neck paragangliomas (HNPGLs) are rare tumors associated with the parasympathetic nervous system. Most are sporadic, but about one third result from germline mutations in succinate dehydrogenase (SDH) genes (SDHB, SDHC, SDHD, SDHA, or SDHAF2). Although a molecular connection between SDH dysfunction and tumor development is still unclear, the most accepted hypothesis proposes a central role of the pseudohypoxic pathway. SDH dysfunction induces abnormal stabilization of the hypoxia-inducible factors (HIFs) that regulate target genes involved in proliferation, apoptosis, angiogenesis, and metabolism. The involvement of these pathways in the development of sporadic HNPGLs is presently unknown.

Objective:
To get some insights into the hypoxic/pseudohypoxic molecular basis of HNPGLs, we attempted to define the gene, microRNA (miRNA), and HIF-1α expression patterns that distinguish tumors from normal paraganglia tissue.

Design:
Genome microarray and TaqMan low-density arrays were used to analyze gene and miRNA expression, respectively, in 17 HNPGL tumor tissues and three normal human carotid bodies. Twelve HNPGLs were used for validation of data. HIF-1α, SDHB, and iron-sulfur cluster scaffold protein (ISCU) protein expression was analyzed by immunohistochemistry.

Results:
We found activation of a canonical HIF-1α-related gene expression signaling only in a subset of HNPGLs from patients that did not harbor germline or somatic SDH mutations. The pseudohypoxic signature consisted in the overexpression of both HIF-1α-target genes and the HIF-1α-inducible miRNA, miR-210, and down-regulation of the miR-210 target gene, ISCU1/2. A decreased level of the iron-sulfur-containing protein SDHB was found by immunohistochemical analysis performed in two of these tumors.

Conclusions:
Collectively, this study unveiled a putative signaling axis of HIF-1α/miRNA-210/ISCU in a subset of HNPGLs that could have an impact on SDHB protein stability by a mechanism independent of SDH mutations, thus providing a foundation to better understand the functional interplay between HIF, miR-210, and mitochondria and its relevance in the pathogenesis of HNPGLs.
Comparative phenotypic analysis of the two major splice isoforms of phosphatidylinositol phosphate kinase type Iγ in vivo
Authors: Legate Kyle R. , Montag Dirk , Böttcher Ralph T. , Takahashi Seiichiro , Fässler Reinhard 
Published: September 2012

Summary
Localized production of polyphosphoinositides is critical for their signaling function. To examine the biological relevance of specific pools of phosphatidylinositol 4,5-bisphosphate we compared the consequences of genetically ablating all isoforms of phosphatidylinositol phosphate (PIP) kinase type Iγ (PIPKIγ), encoded by the gene Pip5k1c, versus ablation of a specific splice isoform, PIPKIγ_i2, with respect to three reported PIPKIγ functions. Ablation of PIPKIγ_i2 caused a neuron-specific endocytosis defect similar to that found in PIPKIγ−/− mice, while agonist-induced calcium signaling was reduced in PIPKIγ−/− cells, but was not affected in the absence of PIPKIγ_i2. A reported contribution of PIPKIγ to epithelial integrity was not evident in PIPKIγ−/− mice. Given that mice lacking PIPKIγ_i2 live a normal lifespan whereas PIPKIγ−/− mice die shortly after birth, we propose that PIPKIγ-mediated metabotropic calcium signaling may represent an essential function of PIPKIγ, whereas functions specific to the PIPKIγ_i2 splice isoform are not essential for survival.
Transcriptional regulation of Profilin during wound closure in Drosophila larvae
Authors: Brock Amanda R. , Wang Yan , Berger Susanne , Renkawitz-Pohl Renate , Han Violet C. , Wu Yujane , Galko Michael J. 
Published: September 2012

Summary
Injury is an inevitable part of life, making wound healing essential for survival. In postembryonic skin, wound closure requires that epidermal cells recognize the presence of a gap and change their behavior to migrate across it. In Drosophila larvae, wound closure requires two signaling pathways [the Jun N-terminal kinase (JNK) pathway and the Pvr receptor tyrosine kinase signaling pathway] and regulation of the actin cytoskeleton. In this and other systems, it remains unclear how the signaling pathways that initiate wound closure connect to the actin regulators that help execute wound-induced cell migrations. Here, we show that chickadee, which encodes the Drosophila Profilin, a protein important for actin filament recycling and cell migration during development, is required for the physiological process of larval epidermal wound closure. After injury, chickadee is transcriptionally upregulated in cells proximal to the wound. We found that JNK, but not Pvr, mediates the increase in chic transcription through the Jun and Fos transcription factors. Finally, we show that chic-deficient larvae fail to form a robust actin cable along the wound edge and also fail to form normal filopodial and lamellipodial extensions into the wound gap. Our results thus connect a factor that regulates actin monomer recycling to the JNK signaling pathway during wound closure. They also reveal a physiological function for an important developmental regulator of actin and begin to tease out the logic of how the wound repair response is organized.
Molecular mechanisms regulating the establishment of hepatocyte polarity during human hepatic progenitor cell differentiation into a functional hepatocyte-like phenotype
Authors: Hua Mingxi , Zhang Weitao , Li Weihong , Li Xueyang , Liu Baoqing , Lu Xin , Zhang Haiyan 
Published: September 2012

Summary
The correct functioning of hepatocytes requires the establishment and maintenance of hepatocyte polarity. However, the mechanisms regulating the generation of hepatocyte polarity are not completely understood. The differentiation of human fetal hepatic progenitor cells (hFHPCs) into functional hepatocytes provides a powerful in vitro model system for studying the molecular mechanisms governing hepatocyte development. In this study, we used a two-stage differentiation protocol to generate functional polarized hepatocyte-like cells (HLCs) from hFHPCs. Global gene expression profiling was performed on triplicate samples of hFHPCs, immature-HLCs and mature-HLCs. When the differential gene expression was compared based on the differentiation stage, a number of genes were identified that might be essential for establishing and maintaining hepatocyte polarity. These genes include those that encode actin filament-binding protein, protein tyrosine kinase activity molecules, and components of signaling pathways, such as PTK7, PARD3, PRKCI and CDC42. Based on known and predicted protein-protein interactions, the candidate genes were assigned to networks and clustered into functional categories. The expression of several of these genes was confirmed using real-time RT-PCR. By inactivating genes using small interfering RNA, we demonstrated that PTK7 and PARD3 promote hepatic polarity formation and affect F-actin organization. These results provide unique insight into the complex process of polarization during hepatocyte differentiation, indicating key genes and signaling molecules governing hepatocyte differentiation.
The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci
Authors: Sudharsan Raghavi , Azuma Yoshiaki 
Published: September 2012

Summary
The small ubiquitin-like modifier (SUMO) ligase PIAS1 (Protein Inhibitor of Activated Stat-1) has been shown to play a role in cellular stress response by SUMOylating several proteins that are involved in DNA repair, apoptosis and transcription. In this paper, we show that PIAS1 regulates ultraviolet (UV)-induced apoptosis by recruiting Death-associated protein 6 (Daxx) to PIAS1-generated SUMO-foci. Cells that ectopically express PIAS1, but not other PIASes, show increased sensitivity to UV irradiation, suggesting that PIAS1 has a distinct function in UV-dependent apoptosis. Domain analysis of PIAS1 indicates that both PIAS1 SUMO-ligase activity and the specific localization of PIAS1 through its N-terminal and C-terminal domains are essential for UV-induced cell death. Daxx colocalizes with PIAS1-generated SUMOylated foci, and the reduction of Daxx using RNAi alleviates UV-induced apoptosis in PIAS1-expressing cells. PIAS1-mediated recruitment of Daxx and apoptosis following UV irradiation are dependent upon the Daxx C-terminal SUMO-interacting motif (SIM). Overall, our data suggest that the pro-apoptotic protein Daxx specifically interacts with one or more substrates SUMOylated by PIAS1 and this interaction leads to apoptosis following UV irradiation.
A key phosphorylation site in AC8 mediates regulation of Ca2+-dependent cAMP dynamics by an AC8–AKAP79–PKA signalling complex
Authors: Willoughby Debbie , Halls Michelle L. , Everett Katy L. , Ciruela Antonio , Skroblin Philipp , Klussmann Enno , Cooper Dermot M. F. 
Published: September 2012

Summary
Adenylyl cyclase (AC) isoforms can participate in multimolecular signalling complexes incorporating A-kinase anchoring proteins (AKAPs). We recently identified a direct interaction between Ca2+-sensitive AC8 and plasma membrane-targeted AKAP79/150 (in cultured pancreatic insulin-secreting cells and hippocampal neurons), which attenuated the stimulation of AC8 by Ca2+ entry (Willoughby et al., 2010). Here, we reveal that AKAP79 recruits cAMP-dependent protein kinase (PKA) to mediate the regulatory effects of AKAP79 on AC8 activity. Modulation by PKA is a novel means of AC8 regulation, which may modulate or apply negative feedback to the stimulation of AC8 by Ca2+ entry. We show that the actions of PKA are not mediated indirectly via PKA-dependent activation of protein phosphatase 2A (PP2A) B56δ subunits that associate with the N-terminus of AC8. By site-directed mutagenesis we identify Ser-112 as an essential residue for direct PKA phosphorylation of AC8 (Ser-112 lies within the N-terminus of AC8, close to the site of AKAP79 association). During a series of experimentally imposed Ca2+ oscillations, AKAP79-targeted PKA reduced the on-rate of cAMP production in wild-type but not non-phosphorylatable mutants of AC8, which suggests that the protein–protein interaction may provide a feedback mechanism to dampen the downstream consequences of AC8 activation evoked by bursts of Ca2+ activity. This fine-tuning of Ca2+-dependent cAMP dynamics by targeted PKA could be highly significant for cellular events that depend on the interplay of Ca2+ and cAMP, such as pulsatile hormone secretion and memory formation.
RIN1 orchestrates the activation of RAB5 GTPases and ABL tyrosine kinases to determine the fate of EGFR
Authors: Balaji Kavitha , Mooser Chelsea , Janson Christine M. , Bliss Joanne M. , Hojjat Houmehr , Colicelli John 
Published: September 2012

Summary
Stimulation of epidermal growth factor receptor (EGFR) initiates RAS signaling simultaneously with EGFR internalization. Endocytosed EGFR is then either recycled or degraded. EGFR fate is determined in part by the RAS effector RIN1, a guanine nucleotide exchange factor (GEF) for RAB5 GTPases. EGFR degradation was slowed by RIN1 silencing, enhanced by RIN1 overexpression and accelerated by RIN1 localization to the plasma membrane. RIN1 also directly activates ABL tyrosine kinases, which regulate actin remodeling, a function not previously connected to endocytosis. We report that RIN1-RAB5 signaling favors EGFR downregulation over EGFR recycling, whereas RIN1-ABL signaling stabilizes EGFR and inhibits macropinocytosis. RIN1QM, a mutant that blocks ABL activation, caused EGF-stimulated membrane ruffling, actin remodeling, dextran uptake and EGFR degradation. An ABL kinase inhibitor phenocopied these effects in cells overexpressing RIN1. EGFR activation also promotes RIN1 interaction with BIN1, a membrane bending protein. These findings suggest that RIN1 orchestrates RAB5 activation, ABL kinase activation and BIN1 recruitment to determine EGFR fate.
Lipid class and depth-specific thermal properties in the blubber of two species of odontocete cetaceans, the short-finned pilot whale (Globicephala macrorhynchus) and the pygmy sperm whale (Kogia breviceps)
Authors: Bagge Laura E. , Koopman Heather N. , Rommel Sentiel A. , McLellan William A. , Pabst D. A. 
Published: September 2012

SummaryBlubber, the specialized hypodermis of cetaceans, provides thermal insulation through the quantity and quality of lipids it contains. Quality refers to % lipid content; however, not all lipids are the same. Certain deep-diving cetacean groups possess blubber with lipids - wax esters (WE) - that are not typically found in mammals, and the insulative quality of “waxy” blubber is unknown. Our study explored the influence of lipid storage class – specifically WE in pygmy sperm whales (Kogia breviceps; n=7) and typical mammalian triacylglycerols (TAG) in short-finned pilot whales (Globicephala macrorhynchus; n=7) – on blubber’s thermal properties. Although the blubber of both species had similar total lipid contents, the thermal conductivity of G. macrorhynchus blubber (0.20 ± 0.01 Wm-1°C-1) was significantly higher than that of K. breviceps (0.15 ± 0.01 Wm-1°C-1; P=0.0006). These results suggest that lipid class significantly influences blubber’s ability to resist heat flow. In addition, because blubber’s lipid content is known to be stratified, we measured its depth-specific thermal conductivities. In K. breviceps blubber, the depth-specific conductivity values tended to vary inversely with lipid content. In contrast, G. macrorhynchus blubber displayed unexpected depth-specific relationships between lipid content and conductivity, which suggests that temperature-dependent effects, such as melting, may be occurring. Differences in heat flux measurements across the depth of the blubber samples provide evidence that both species are capable of storing heat in their blubber. The function of blubber as an insulator is complex and may rely upon its lipid class, stratified composition, and dynamic heat storage capabilities.