Lipolysis and lipophagy play individual and interactive roles in regulating triacylglycerol and cholesterol homeostasis and mitochondrial form in zebrafish

Neutral lipases-mediated lipolysis and acid lipases-moderated lipophagy are two main processes for degradation of lipid droplets (LDs). However, the individual and interactive roles of these metabolic pathways are not well known across vertebrates. This study explored the roles of lipolysis and lipophagy from the aspect of neutral and acid lipases in zebrafish. We established zebrafish strains deficient in either adipose triglyceride lipase (atgl^?/?; AKO fish) or lysosomal acid lipase (lal^?/?; LKO fish) respectively, and then inhibited lipolysis in the LKO fish and lipophagy in the AKO fish by feeding diets supplemented with the corresponding inhibitors Atglistatin and 3-Methyladenine, respectively. Both the AKO and LKO fish showed reduced growth, swimming activity, and oxygen consumption. The AKO fish did not show phenotypes in adipose tissue, but mainly accumulated triacylglycerol (TAG) in liver, also, they had large LDs in the hepatocytes, and did not stimulate lipophagy as a compensation response but maintained basal lipophagy. The LKO fish reduced total lipid accumulation in the body but had high cholesterol content in liver; also, they accumulated small LDs in the hepatocytes, and showed increased lipolysis, especially Atgl expression, as a compensatory mechanism. Simultaneous inhibition of lipolysis and lipophagy in zebrafish resulted in severe liver damage, with the potential to trigger mitophagy. Overall, our study illustrates that lipolysis and lipophagy perform individual and interactive roles in maintaining homeostasis of TAG and cholesterol metabolism. Furthermore, the interactive roles of lipolysis and lipophagy may be essential in regulating the functions and form of mitochondria.     

Strontium stratigraphy of the Oligocene–Early Miocene shellbeds of the Kutch Basin,western India,and its implications

The Kutch Basin is unique among the western Indian sedimentary basins because of its near-complete sequence of post-Palaeozoic rocks. Due to extensive marine influence, the Oligocene–Early Miocene formations of the basin, namely Maniyara Fort, Khari Nadi and Chhasra, contain numerous shellbeds. Although age assignments of these formations exist based on foraminiferal biostratigraphy, detailed numerical age of the lithounits are yet to be established. We have identified a total of eleven distinct shellbeds (oldest SB 01 to youngest SB11) from this interval primarily containing bivalve fossils. Using ⁸⁷Sr/⁸⁶Sr of selected oyster and pectinid shells with pristine shell characteristics, we report the age of four shellbeds. The ages of SB 01, SB 04, SB 06 and SB 10 are 24.37, 17.31, 16.85 and 15.38 Ma, respectively. Our dates suggest a Chattian (24.37 Ma) age for SB 01 from the Bermoti Member, validating the previous biostratigraphical estimates from the Maniyara Fort Formation. The Chhasra Formation, however, shows a younger range of ages (17.31–15.38 Ma) characterized by a transition from the Burdigalian (SB 04–SB 06) to the Langhian (SB 10) stages. These dates have important implications in the study of sequence stratigraphy, Palaeobiogeography and tectonic history of the Kutch Basin. A surface with subaerial exposure is found in SB 08 (between 16.85 and 15.38 Ma) that corresponds to a global eustatic sea-level decrease (Mi2). Our new dates will also help evaluate the response of marine fauna to the closure of the Tethyan seaway around 19 Ma due to the formation of ‘Gomphotherium Landbridge’. The dated shellbeds enable us to identify pre- and post-closure fauna and assess the effect of biogeographical separation on these fauna. These dates have important implications in evaluating the regional geological record of western India in the context of various global events.     

Optimization of process parameters for ethanol production from sugar cane molasses by Zymomonas mobilis using response surface methodology and genetic algorithm

Ethanol is a potential energy source and its production from renewable biomass has gained lot of popularity. There has been worldwide research to produce ethanol from regional inexpensive substrates. The present study deals with the optimization of process parameters (viz. temperature, pH, initial total reducing sugar (TRS) concentration in sugar cane molasses and fermentation time) for ethanol production from sugar cane molasses by Zymomonas mobilis using Box–Behnken experimental design and genetic algorithm (GA). An empirical model was developed through response surface methodology to analyze the effects of the process parameters on ethanol production. The data obtained after performing the experiments based on statistical design was utilized for regression analysis and analysis of variance studies. The regression equation obtained after regression analysis was used as a fitness function for the genetic algorithm. The GA optimization technique predicted a maximum ethanol yield of 59.59 g/L at temperature 31 °C, pH 5.13, initial TRS concentration 216 g/L and fermentation time 44 h. The maximum experimental ethanol yield obtained after applying GA was 58.4 g/L, which was in close agreement with the predicted value.     

The Cell Collective: Toward an open and collaborative approach to systems biology

Background

The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression.

Results

In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU.

Conclusions

The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.     

TNFα regulates the localization of CD40 in lipid rafts of glioma cells

Resistance of glioblastoma multiforme (GBM) to TNFα induced apoptosis is attributed to NFκB activation. As TNF-receptor family member CD40 regulates NFκB activation, we investigated the role of CD40 in NFκB activation in GBM. We observed elevated CD40 levels in human glioma samples as compared to the surrounding normal tissue. Treatment with TNFα elevated CD40 levels in glioma cells and inhibition of CD40 signaling failed to abrogate TNFα induced NFκΒ activity. While TNFα increased the interaction between TRAF2/6, IκBα, IKKα/β in the CD40 signalosome, the level of CD40 in the signalosome remained unaffected upon TNFα treatment. Interestingly, TNFα decreased the spatial localization of CD40 and increased TRAF2/6 co-localization with lipid raft marker Caveolin. As localization of CD40 signalosome in lipid raft is crucial for NFκB activation, TNFα mediated decreased clustering of CD40 in lipid rafts could have possibly contributed to its non-involvement in NFκB activation.     

Do GGA Adaptors Bind Internal DXXLL Motifs?

The GGA family of clathrin adaptor proteins mediates the intracellular trafficking of transmembrane proteins by interacting with DXXLL-type sorting signals on the latter. These signals were originally identified at the carboxy-termini of the transmembrane cargo proteins. Subsequent studies, however, showed that internal DXXLL sorting motifs occur within the N- or C-terminal cytoplasmic domains of cargo molecules. The GGAs themselves also contain internal DXXLL motifs that serve to auto-regulate GGA function. A recent study challenged the notion that internal DXXLL signals are competent for binding to GGAs. Since the question of whether GGA adaptors interact with internal DXXLL motifs is fundamental to the identification of bona fide GGA cargo, and to an accurate understanding of GGA regulation within cells, we have extended our previous findings. We now present additional evidence confirming that GGAs do interact with internal DXXLL motifs. We also summarize the recent reports from other laboratories documenting internal GGA binding motifs.     

Nuclear co-translocation of myotrophin and p65 stimulates myocyte growth. Regulation by myotrophin hairpin loops

Myotrophin, a 12-kDa ankyrin repeat protein, stimulates protein synthesis and cardiomyocyte growth to initiate cardiac hypertrophy by activating the NF-kappaB signaling cascade. We found that, after internalization into myocytes, myotrophin cotranslocates into the nucleus with p65 to stimulate myocyte growth. We used structure-based mutations on the hairpin loops of myotrophin to determine the effect of the loops on myotrophin and p65 localization, induction of protein synthesis, and cardiac hypertrophy. Loop mutants, most prominently glutamic acid 33-->alanine (E33A), stimulated protein synthesis much less than wild type. Myotrophin-E33A internalized into myocytes but did not translocate into the nucleus and failed to promote nuclear translocation of p65. In addition, two cardiac hypertrophy marker genes, atrial natriuretic factor and beta-myosin heavy chain, were not up-regulated in E33A-treated cells. Myotrophin-induced myocyte growth and initiation of hypertrophy thus require nuclear co-translocation of myotrophin and p65, in a manner that depends crucially on the myotrophin hairpin loops.     

Mechanism of ubiquitin recognition by the CUE domain of Vps9p

Coupling of ubiquitin conjugation to ER degradation (CUE) domains are approximately 50 amino acid monoubiquitin binding motifs found in proteins of trafficking and ubiquitination pathways. The 2.3 A structure of the Vps9p-CUE domain is a dimeric domain-swapped variant of the ubiquitin binding UBA domain. The 1.7 A structure of the CUE:ubiquitin complex shows that one CUE dimer binds one ubiquitin molecule. The bound CUE dimer is kinked relative to the unbound CUE dimer and wraps around ubiquitin. The CUE monomer contains two ubiquitin binding surfaces on opposite faces of the molecule that cannot bind simultaneously to a single ubiquitin molecule. Dimerization of the CUE domain allows both surfaces to contact a single ubiquitin molecule, providing a mechanism for high-affinity binding to monoubiquitin.     

Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell

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