PaperPlayer biorxiv molecular biology

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.25.220095v1?rss=1

Authors: Garrido-Godino, A. I., Gupta, I., Gutierrez-Santiago, F., Martinez-Padilla, A. B., Alekseenko, A., Steinmetz, L. M., Perez-Ortin, J. E., Pelechano, V., Navarro, F.

Abstract:

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analyzed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.24.219584v1?rss=1

Authors: McIntyre, R. L., Denis, S. W., Kamble, R., Petr, M., Schomakers, B. V., Jongejan, A., Scheibye-Knudsen, M., Houtkooper, R. H., Janssens, G. E.

Abstract:

Transcriptome-based drug screening is emerging as a powerful tool to identify geroprotective compounds to intervene in age-related disease. We hypothesized that, by mimicking the transcriptional signature of the highly conserved longevity intervention of FOXO3 (daf-16 in worms) overexpression, we could identify and repurpose compounds with similar downstream effects to increase longevity. Our in silico screen, utilizing the LINCS transcriptome database of genetic and compound interventions, identified several FDA-approved compounds that activate FOXO downstream targets in mammalian cells. These included the neuromuscular blocker atracurium, which also robustly extends both lifespan and healthspan in C. elegans. This longevity is dependent on both daf-16 signaling and inhibition of the neuromuscular acetylcholine receptor. Other neuromuscular blockers tubocurarine and pancuronium caused similar healthspan benefits. We demonstrate nuclear localization of DAF-16 upon atracurium treatment, and, using RNAseq transcriptomics, identify activation of DAF-16 downstream effectors. Together, these data demonstrate the capacity to mimic genetic lifespan interventions with drugs, and in doing so, reveal that the neuromuscular acetylcholine receptor regulates the highly conserved FOXO/DAF-16 longevity pathway.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.217612v1?rss=1

Authors: Gregor, A., Pignitter, M., Fahrngruber, C., Bayer, S., Somoza, V., Koenig, J., Duszka, K.

Abstract:

Our previous study indicated increased levels of taurine-conjugated bile acids in the intestine content of caloric restriction (CR) mice. In the current project, we found increased levels of free taurine and taurine conjugates, including glutathione (GSH)-taurine, in CR compared to ad libitum fed animals in the mucosa along the intestine while there was no impact on taurine and its conjugates in the liver. The levels of free GSH were decreased in the intestine of CR compared to ad libitum fed mice. However, the levels of oxidized GSH were not affected and were complemented by the lack of changes in the antioxidative parameters. Glutathione-S transferases (GST) enzymatic activity was increased as was the expression of GST genes along the GI tract of CR mice. In CR intestine addition of GSH to taurine solution enhanced taurine uptake. Accordingly, the expression of taurine transporter (TauT) was increased in the ileum of CR mice.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.217927v1?rss=1

Authors: Nikolopoulos, G., Smith, C. E. L., Poulter, J. A., Murillo, G., Silva, S., Brown, C. J., Day, P. F., Soldani, F., Al-Bahlani, S., Harris, S. A., O'Connell, M. J., Inglehearn, C. F., Mighell, A. J.

Abstract:

Amelogenesis imperfecta (AI) describes a heterogeneous group of developmental enamel defects that typically have Mendelian inheritance. Exome sequencing of ten families with recessive hypomaturation AI revealed 4 novel and 1 known variants in the matrix metallopeptidase 20 (MMP20) gene that were predicted to be pathogenic. MMP20 encodes a protease that cleaves the developing extracellular enamel matrix and is necessary for normal enamel crystal growth during amelogenesis. New homozygous missense changes were shared between four families of Pakistani heritage (c.625G>C; p.(E209Q)) and two of Omani origin (c.710C>A; p.(S237Y)). In two families of UK origin and one from Costa Rica, affected individuals were homozygous for the previously reported c.954-2A>T; p.(I319Ffs*19) variant. For each of these variants, microsatellite haplotypes appeared to exclude a recent founder effect, but elements of haplotype were conserved, suggesting more distant founding ancestors. New compound heterozygous changes were identified in one family of European heritage; c.809_811+12delACGgtaagattattainsCCAG; p.(?) and c.1122A>C; p.(Q374H). All four new variants are within the zinc dependant peptidase domain. This report further elucidates the mutation spectrum of MMP20 and the probable impact on protein function, confirms a consistent hypomaturation phenotype and shows that mutations in MMP20 are a common cause of autosomal recessive AI in some communities.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218263v1?rss=1

Authors: Ponvert, N. D., Johnson, M. A.

Abstract:

Reproductive isolation leads to the evolution of distinct new species, however, the molecular mechanisms that promote and maintain reproductive barriers are elusive. In flowering plants sperm cells are immotile and are delivered to female gametes by the pollen grain which germinates a polarized extension, the pollen tube, into floral tissue. After growing via polar extension to the female gametophyte, the pollen tube signals with receptive female cells flanking the egg in two distinct steps. If signaling is successful, the pollen tube releases sperm cells for fusion with female gametes. To better understand cell-cell recognition during reproduction, we investigated calcium ion dynamics associated with interspecific cell signaling between mating partners. We observed that interspecific pollen tubes successfully complete initial cell-cell signaling, but fail during later phases of pollen tube reception. Our work refines our understanding of pollen tube reception as a critical block to interspecific hybridization. Our results also shed light on the functional significance of the two phases of pollen tube reception, and implicate the second step as being the stage during which the pollen tube presents its genetic identity.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218156v1?rss=1

Authors: Cui, z., Huntley, R. B., Schultes, N. P., Kakar, k. U., Zeng, Q.

Abstract:

Erwinia amylovora causes fire blight on rosaceous plants. Flower surfaces are the primary location in the fire blight infection pathway. Here E. amylovora proliferates on stigmatic and hypanthium surfaces as epiphytic growth, followed by subsequent endophytic (intercellular) infection in the hypanthium. The type III secretion system (T3SS) is an important virulence factor in E. amylovora. Although the role of T3SS during the endophytic infection is well characterized, its expression during the epiphytic colonization and role in the subsequent infection is less understood. Here, we investigated the T3SS expression in epiphytic E. amylovora on stigma and hypanthium of apple flowers, under different relative humidities (RH). On stigma surfaces, T3SS was expressed in a high percentage of E. amylovora cells, and its expression promotes epiphytic growth. On hypanthium surfaces however, T3SS was expressed in fewer E. amylovora cells than on the stigma, and displayed no correlation with epiphytic growth, even though T3SS expression is essential for infection. E. amylovora cells grown on stigmatic surfaces and then flushed down to the hypanthium displayed a higher level of T3SS expression than cells grown on the hypanthium surface alone. Furthermore, cells pre-cultured on stigma before inoculation on hypanthium caused more infections than cells pre-cultured in a T3SS-repressive medium then used as inoculum, suggesting that the T3SS induction during the stigmatic epiphytic colonization may be beneficial for the subsequent infection. Finally, the epiphytic expression of T3SS is influenced by RH. Higher percentage of stigmatic E. amylovora cells expressed T3SS under high RH than under low RH.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218479v1?rss=1

Authors: Macher, J.-N., van der Hoorn, B. B., Peijnenburg, K., van Walraven, L., Renema, W.

Abstract:

Zooplankton are key players in marine ecosystems, linking primary production to higher trophic levels. The high abundance and high taxonomic diversity renders zooplankton ideal for biodiversity monitoring. However, taxonomic identification of the zooplankton assemblage is challenging due to its high diversity, subtle morphological differences and the presence of many meroplanktonic species, especially in coastal seas. Molecular techniques such as metabarcoding can help with rapid processing and identification of taxa in complex samples, and are therefore promising tools for identifying zooplankton communities. In this study, we applied metabarcoding of the mitochondrial cytochrome c oxidase I gene to zooplankton samples collected along a latitudinal transect in the North Sea, a shelf sea of the Atlantic Ocean. Northern regions of the North Sea are influenced by inflow of oceanic Atlantic waters, whereas the southern parts are characterised by more coastal waters. Our metabarcoding results indicated strong differences in zooplankton community composition between northern and southern areas of the North Sea, particularly in the classes Copepoda, Actinopterygii (ray-finned fishes) and Polychaeta. We compared these results to the known distributions of species reported in previous studies, and by comparing the abundance of copepods to data obtained from the Continuous Plankton Recorder (CPR). We found that our metabarcoding results are mostly congruent with the reported distribution and abundance patterns of zooplankton species in the North Sea. Our results highlight the power of metabarcoding to rapidly assess complex zooplankton samples, and we suggest that the technique could be used in future monitoring campaigns and biodiversity assessments.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218107v1?rss=1

Authors: Biswas, B., Laha, B., Ghosh, M.

Abstract:

The host-parasite interaction is a complex molecular cross-talk between the host and its parasites, where the parasite employs a repertoire of surface and secretory effector molecules for host cell manipulation and successful parasitism. Identification and functional analysis of such parasite specific effectors is an efficient approach to understand the molecular basis of host-parasite interaction which provides us a potential drug target against the parasitic diseases. The current study recognizes an Amastine like Surface Protein (ALSP), present and expressed in abundant amount in intracellular amastigotes form of Leishmania donovani, the causative agent of visceral leishmaniasis. In-silico analysis indicates that this protein is localized in the cytosol of the amastigotes. Characterization of the protein is performed through Indirect ELISA, Immunoprecipitation, MALDI-TOF, MALDI-TOF-MS-MS analysis and subcellular localization. MALDI-TOF MS analysis reveals that the molecular mass of the protein is 10.147 kDa. Following digestion with trypsin, MALDI-TOF-MS-MS analysis using peptide fragments of the purified native protein in amastigotes shows 100% identity with the leishmanial ALSP. Prediction of its presence and expression was done by localization and transcript level studies. Based on in-silico study, ALSP is has been hypothesized to serve as a source of energy for the intracellular parasite during parasitism by conversion of triglycerides into glycerol and fatty acid, assigning a role in virulence through triglyceride lipase activity. The intracellular survival of the parasite with the intervention of the target protein may help in harnessing the candidate molecule, as an appealing target for design of novel chemotherapeutics against visceral leishmaniasis in future.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.24.214544v1?rss=1

Authors: Gimenez, C. A., Curti, L., Hyon, S. H., Grosembacher, L., ROSS, P. J., Pereyra-Bonnet, F.

Abstract:

CRISPR-based systems for epigenetic editing are promising molecular tools that could be harnessed for directed differentiation of pluripotent stem cells. We used the CRISPR/dCas9-VP160, CRISPR/dCas9-TET1 and CRISPR/dCas9-P300 systems for multiplex epigenetic editing and activation of human beta-pancreatic genes (PDX1, NEUROG3, PAX4 and INS). The CRISPR/dCas9-P300 system was the most effective at activating genes with reduced number of sgRNA. Using small number of sgRNA per gene was important to induce multiplex gene activation. Combined activation of transcription factors (TFs) involved in beta cell development resulted in INS gene expression; in which sequential TFs activation was more effective than simultaneous activation. Full CRISPR RNA-based delivery system was able to activate all targeted genes. Overall, this study shows the utility of CRISPR tools for epigenetic editing and directed cellular differentiation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.217307v1?rss=1

Authors: Kurup, K., Mann, S. N., Jackson, J., Matyi, S., Ranjo-Bishop, M., Freeman, W. M., Stout, M. B., Richardson, A., Unnikrishnan, A.

Abstract:

Nutritional manipulations early in life have been shown to influence growth rate and elicit long lasting effects which in turn has been found to impact lifespan. Therefore, we studied the long-term effects of pre-weaning dietary restriction implemented by litter expansion (4, 6, 8, 10, and 12 pups per dam: LS4, LS6, LS8, LS10, LS12) on male and female C57BL/6 mice. After weaning, these mice were fed ad libitum a commercial lab chow for the 15-month duration of the study. The mice from large litter sizes (LS12) were significantly leaner and had reduced total fat mass compared to the normal size litters (LS 6) starting from weaning through to 15 months of age. Male LS10 & 12 mice showed significant reduction in their fat depot masses at 15 months of age: gonadal, subcutaneous, and brown fat whereas the females did not mimic these findings. At 9 months of age, both male and female LS10 and 12 mice showed improved glucose tolerance; however, only male LS10 and LS12 mice showed improved insulin tolerance starting at 5 months of age. In addition, we found that the male LS8, 10 & 12 mice at 15 months of age showed significantly reduced IGF-1 levels in the serum and various other organs (liver, gastrocnemius and brain cortex). Interestingly, the female LS8, 10, 12 mice showed a different pattern with reduced IGF-1 levels in serum, liver and gastrocnemius but not in the brain cortex. Similarly, the litter expanded mice showed sexual divergence in levels of FGF21 and adiponectin with only the male mice showing increased FGF21 and adiponectin levels at 15 months of age. In summary, our data show that, litter expansion results in long-lasting metabolic changes that are age and sex dependent with the male mice showing an early and robust response compared to female mice.

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