cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378856.v1
title: Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (<i>Equisetum arvense</i>)

description: Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (<i>Equisetum arvense</i>) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
DOI: 10.6084/m9.figshare.1378856.v3
title: Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (<i>Equisetum arvense</i>)

description: Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (<i>Equisetum arvense</i>) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
DOI: 10.6084/m9.figshare.1378854
title: Mitophagy is primarily due to alternative autophagy and requires the MAPK1 and MAPK14 signaling pathways

description: In cultured cells, not many mitochondria are degraded by mitophagy induced by physiological cellular stress. We observed mitophagy in HeLa cells using a method that relies on the pH-sensitive fluorescent protein Keima. With this approach, we found that mitophagy was barely induced by carbonyl cyanide m-chlorophenyl hydrazone treatment, which is widely used as an inducer of PARK2/Parkin-related mitophagy, whereas a small but modest amount of mitochondria were degraded by mitophagy under conditions of starvation or hypoxia. Mitophagy induced by starvation or hypoxia was marginally suppressed by knockdown of ATG7 and ATG12, or MAP1LC3B, which are essential for conventional macroautophagy. In addition, mitophagy was efficiently induced in <i>Atg5</i> knockout mouse embryonic fibroblasts. However, knockdown of RAB9A and RAB9B, which are essential for alternative autophagy, but not conventional macroautophagy, severely suppressed mitophagy. Finally, we found that the MAPKs MAPK1/ERK2 and MAPK14/p38 were required for mitophagy. Based on these findings, we conclude that mitophagy in mammalian cells predominantly occurs through an alternative autophagy pathway, requiring the MAPK1 and MAPK14 signaling pathways.
DOI: 10.6084/m9.figshare.1378856.v2
title: Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (<i>Equisetum arvense</i>)

description: Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (<i>Equisetum arvense</i>) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
DOI: 10.6084/m9.figshare.1378854.v1
title: Mitophagy is primarily due to alternative autophagy and requires the MAPK1 and MAPK14 signaling pathways

description: In cultured cells, not many mitochondria are degraded by mitophagy induced by physiological cellular stress. We observed mitophagy in HeLa cells using a method that relies on the pH-sensitive fluorescent protein Keima. With this approach, we found that mitophagy was barely induced by carbonyl cyanide m-chlorophenyl hydrazone treatment, which is widely used as an inducer of PARK2/Parkin-related mitophagy, whereas a small but modest amount of mitochondria were degraded by mitophagy under conditions of starvation or hypoxia. Mitophagy induced by starvation or hypoxia was marginally suppressed by knockdown of ATG7 and ATG12, or MAP1LC3B, which are essential for conventional macroautophagy. In addition, mitophagy was efficiently induced in <i>Atg5</i> knockout mouse embryonic fibroblasts. However, knockdown of RAB9A and RAB9B, which are essential for alternative autophagy, but not conventional macroautophagy, severely suppressed mitophagy. Finally, we found that the MAPKs MAPK1/ERK2 and MAPK14/p38 were required for mitophagy. Based on these findings, we conclude that mitophagy in mammalian cells predominantly occurs through an alternative autophagy pathway, requiring the MAPK1 and MAPK14 signaling pathways.
DOI: 10.6084/m9.figshare.1378847
title: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014

description: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014
DOI: 10.6084/m9.figshare.1378847.v2
title: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014

description: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014
DOI: 10.6084/m9.figshare.1378847.v1
title: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014

description: Comment on ‘Late Cretaceous extension and Palaeogene rotation-related contraction in Central Anatolia recorded in the Ayhan-Büyükkışla basin’ by Advokaat <i>et al.</i> 2014
DOI: 10.6084/m9.figshare.1378829
title: Unveiling the principle of microRNA-mediated redundancy in cellular pathway regulation

description: Understanding the multifaceted nature of microRNA (miRNA) function in mammalian cells is still a challenge. Commonly accepted principles of cooperativity and multiplicity of miRNA function imply that individual mRNAs can be targeted by several miRNAs whereas a single miRNA may concomitantly regulate a subset of different genes. However, there is a paucity of information whether multiple miRNAs regulate critical cellular events and thereby acting redundantly. To gain insight into this notion, we conducted an unbiased high-content miRNA screen by individually introducing 1139 miRNA mimics into Chinese hamster ovary (CHO) cells. We discovered that 66% of all miRNAs significantly impacted on proliferation, protein expression, apoptosis and necrosis. In summary, we provide evidence for a substantial degree of redundancy among miRNAs to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1378827
title: Probing the closed-loop model of mRNA translation in living cells

description: The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence <i>in vivo</i> is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
DOI: 10.6084/m9.figshare.1378828
title: Regulation of human <i>PTCH1b</i> expression by different 5' untranslated region <i>cis</i>-regulatory elements

description: <i>PTCH1</i> gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. <i>PTCH1</i> germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for <i>PTCH1</i> haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore <i>cis</i>-regulatory elements in the 5'UTR of <i>PTCH1</i> transcript 1b. The (CGG)<sub>n</sub> polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of <i>PTCH1b</i> mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR <i>PTCH1b cis</i>-element features in the regulation of the Hedgehog-Gli signaling pathway.
DOI: 10.6084/m9.figshare.1378829.v1
title: Unveiling the principle of microRNA-mediated redundancy in cellular pathway regulation

description: Understanding the multifaceted nature of microRNA (miRNA) function in mammalian cells is still a challenge. Commonly accepted principles of cooperativity and multiplicity of miRNA function imply that individual mRNAs can be targeted by several miRNAs whereas a single miRNA may concomitantly regulate a subset of different genes. However, there is a paucity of information whether multiple miRNAs regulate critical cellular events and thereby acting redundantly. To gain insight into this notion, we conducted an unbiased high-content miRNA screen by individually introducing 1139 miRNA mimics into Chinese hamster ovary (CHO) cells. We discovered that 66% of all miRNAs significantly impacted on proliferation, protein expression, apoptosis and necrosis. In summary, we provide evidence for a substantial degree of redundancy among miRNAs to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1378829.v3
title: Unveiling the principle of microRNA-mediated redundancy in cellular pathway regulation

description: Understanding the multifaceted nature of microRNA (miRNA) function in mammalian cells is still a challenge. Commonly accepted principles of cooperativity and multiplicity of miRNA function imply that individual mRNAs can be targeted by several miRNAs whereas a single miRNA may concomitantly regulate a subset of different genes. However, there is a paucity of information whether multiple miRNAs regulate critical cellular events and thereby acting redundantly. To gain insight into this notion, we conducted an unbiased high-content miRNA screen by individually introducing 1139 miRNA mimics into Chinese hamster ovary (CHO) cells. We discovered that 66% of all miRNAs significantly impacted on proliferation, protein expression, apoptosis and necrosis. In summary, we provide evidence for a substantial degree of redundancy among miRNAs to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1378828.v1
title: Regulation of human <i>PTCH1b</i> expression by different 5' untranslated region <i>cis</i>-regulatory elements

description: <i>PTCH1</i> gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. <i>PTCH1</i> germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for <i>PTCH1</i> haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore <i>cis</i>-regulatory elements in the 5'UTR of <i>PTCH1</i> transcript 1b. The (CGG)<sub>n</sub> polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of <i>PTCH1b</i> mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR <i>PTCH1b cis</i>-element features in the regulation of the Hedgehog-Gli signaling pathway.
DOI: 10.6084/m9.figshare.1378829.v2
title: Unveiling the principle of microRNA-mediated redundancy in cellular pathway regulation

description: Understanding the multifaceted nature of microRNA (miRNA) function in mammalian cells is still a challenge. Commonly accepted principles of cooperativity and multiplicity of miRNA function imply that individual mRNAs can be targeted by several miRNAs whereas a single miRNA may concomitantly regulate a subset of different genes. However, there is a paucity of information whether multiple miRNAs regulate critical cellular events and thereby acting redundantly. To gain insight into this notion, we conducted an unbiased high-content miRNA screen by individually introducing 1139 miRNA mimics into Chinese hamster ovary (CHO) cells. We discovered that 66% of all miRNAs significantly impacted on proliferation, protein expression, apoptosis and necrosis. In summary, we provide evidence for a substantial degree of redundancy among miRNAs to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1378828.v3
title: Regulation of human <i>PTCH1b</i> expression by different 5' untranslated region <i>cis</i>-regulatory elements

description: <i>PTCH1</i> gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. <i>PTCH1</i> germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for <i>PTCH1</i> haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore <i>cis</i>-regulatory elements in the 5'UTR of <i>PTCH1</i> transcript 1b. The (CGG)<sub>n</sub> polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of <i>PTCH1b</i> mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR <i>PTCH1b cis</i>-element features in the regulation of the Hedgehog-Gli signaling pathway.
DOI: 10.6084/m9.figshare.1378828.v2
title: Regulation of human <i>PTCH1b</i> expression by different 5' untranslated region <i>cis</i>-regulatory elements

description: <i>PTCH1</i> gene codes for a 12-pass transmembrane receptor with a negative regulatory role in the Hedgehog-Gli signaling pathway. <i>PTCH1</i> germline mutations cause Gorlin syndrome, a disorder characterized by developmental abnormalities and tumor susceptibility. The autosomal dominant inheritance, and the evidence for <i>PTCH1</i> haploinsufficiency, suggests that fine-tuning systems of protein patched homolog 1 (PTC1) levels exist to properly regulate the pathway. Given the role of 5' untranslated region (5'UTR) in protein expression, our aim was to thoroughly explore <i>cis</i>-regulatory elements in the 5'UTR of <i>PTCH1</i> transcript 1b. The (CGG)<sub>n</sub> polymorphism was the main potential regulatory element studied so far but with inconsistent results and no clear association between repeat number and disease risk. Using luciferase reporter constructs in human cell lines here we show that the number of CGG repeats has no strong impact on gene expression, both at mRNA and protein levels. We observed variability in the length of 5'UTR and changes in abundance of the associated transcripts after pathway activation. We show that upstream AUG codons (uAUGs) present only in longer 5'UTRs could negatively regulate the amount of PTC1 isoform L (PTC1-L). The existence of an internal ribosome entry site (IRES) observed using different approaches and mapped in the region comprising the CGG repeats, would counteract the effect of the uAUGs and enable synthesis of PTC1-L under stressful conditions, such as during hypoxia. Higher relative translation efficiency of <i>PTCH1b</i> mRNA in HEK 293T cultured hypoxia was observed by polysomal profiling and Western blot analyses. All our results point to an exceptionally complex and so far unexplored role of 5'UTR <i>PTCH1b cis</i>-element features in the regulation of the Hedgehog-Gli signaling pathway.
DOI: 10.6084/m9.figshare.1378827.v4
title: Probing the closed-loop model of mRNA translation in living cells

description: The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence <i>in vivo</i> is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression.
DOI: 10.6084/m9.figshare.1378818
title: Tree retention practices in boreal forests: what kind of future landscapes are we creating?

description: Tree retention practices promoting biodiversity may reshape future boreal forest production landscapes. Using the Heureka system, scenarios of 0%, 5%, and 20% retained patches at the stand level were projected over 200 years in a 533 ha boreal landscape. Visualizations of future forest states at a landscape scale and a more detailed scale were made based on the projections. The no retention results in no forest &gt;120 years old, and no large trees (diameter at breast height &gt;40 cm for conifers and &gt;35 cm for broadleaved trees) 100 years from now. With retention levels of 5% and 20%, the area of old forest will comprise 7% and 19% of the total area, respectively. The average number of large trees per ha will be 4 and 13, respectively. Deadwood volumes will be 2.5 times higher at 5% retention and 4 times higher at 20% retention compared to no retention. Landscape visualizations indicate that retention patches covering 5% will marginally modify the visual impression, compared to clear-cuts, while 20% cover will create a much more varied landscape. We conclude that the retention approach is essential for restoring natural conditions. Landscape transformation will be slow and depend on starting conditions and retention levels.
DOI: 10.6084/m9.figshare.1378818.v2
title: Tree retention practices in boreal forests: what kind of future landscapes are we creating?

description: Tree retention practices promoting biodiversity may reshape future boreal forest production landscapes. Using the Heureka system, scenarios of 0%, 5%, and 20% retained patches at the stand level were projected over 200 years in a 533 ha boreal landscape. Visualizations of future forest states at a landscape scale and a more detailed scale were made based on the projections. The no retention results in no forest &gt;120 years old, and no large trees (diameter at breast height &gt;40 cm for conifers and &gt;35 cm for broadleaved trees) 100 years from now. With retention levels of 5% and 20%, the area of old forest will comprise 7% and 19% of the total area, respectively. The average number of large trees per ha will be 4 and 13, respectively. Deadwood volumes will be 2.5 times higher at 5% retention and 4 times higher at 20% retention compared to no retention. Landscape visualizations indicate that retention patches covering 5% will marginally modify the visual impression, compared to clear-cuts, while 20% cover will create a much more varied landscape. We conclude that the retention approach is essential for restoring natural conditions. Landscape transformation will be slow and depend on starting conditions and retention levels.