1,209,743 Works

Text-analysis reveals taxonomic and geographic disparities in animal pollination literature

Joseph Millard, Robin Freeman & Tim Newbold
Frequency of animal genera in English, primary research abstracts returned by Scopus with the term "pollinat*".
We used the named entity recognition algorithms Taxonfinder and Neti Neti in the R package 'taxize' to extract taxonomic records from "pollinat*" abstracts downloaded from Scopus. We then used the geoparser CLIFF-CLAVIN to geoparse geographic locations and geographic focus.
Please see "Millard et al (in prep.), Text-analysis reveals taxonomic and geographic disparities in animal pollination literature" for a detailed methodology.

Text-analysis reveals taxonomic and geographic disparities in animal pollination literature

Joseph Millard, Robin Freeman & Tim Newbold
Frequency of animal genera in English, primary research abstracts returned by Scopus with the term "pollinat*".
We used the named entity recognition algorithms Taxonfinder and Neti Neti in the R package 'taxize' to extract taxonomic records from "pollinat*" abstracts downloaded from Scopus. We then used the geoparser CLIFF-CLAVIN to geoparse geographic locations and geographic focus.
Please see "Millard et al (in prep.), Text-analysis reveals taxonomic and geographic disparities in animal pollination literature" for a detailed methodology.

Synthesis of some novel 5-substituted benzamido-6-arylamino-pyrazolo[3,4-D]pyrimidin-4-one derivatives for herbicidal activity

Jin Luo, Shu Li, Qiongwen Kang, Yi Sun & Tao Wang
Sixteen novel 3-methylthio-5-substituted benzamido-6-arylamino-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one derivatives (4a–p) were successfully synthesized from iminophosphoranes, aryl isocyanate, and substituted benzoylhydrazine. The structures of the title compounds were elucidated by FT-IR, 1H NMR, 13C NMR, and HRMS. Herbicidal activity of the compounds 4a–p against Brassica napus (rape), Echinochloa crusgalli (barnyard grass), Cucumis sativus (cucumber), and Triticum aestivum (wheat) were determined. The results showed that 5-(2-chlorobenzamido)-6-phenylamino-3-methylthio-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one (4c) displayed remarkable inhibition activity against the stalk and root of rape with...

Synthesis of some novel 5-substituted benzamido-6-arylamino-pyrazolo[3,4-D]pyrimidin-4-one derivatives for herbicidal activity

Jin Luo, Shu Li, Qiongwen Kang, Yi Sun & Tao Wang
Sixteen novel 3-methylthio-5-substituted benzamido-6-arylamino-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one derivatives (4a–p) were successfully synthesized from iminophosphoranes, aryl isocyanate, and substituted benzoylhydrazine. The structures of the title compounds were elucidated by FT-IR, 1H NMR, 13C NMR, and HRMS. Herbicidal activity of the compounds 4a–p against Brassica napus (rape), Echinochloa crusgalli (barnyard grass), Cucumis sativus (cucumber), and Triticum aestivum (wheat) were determined. The results showed that 5-(2-chlorobenzamido)-6-phenylamino-3-methylthio-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one (4c) displayed remarkable inhibition activity against the stalk and root of rape with...

Comparison between cytoarchitectonic and MRI based parcellation of the human auditory cortex

Omer Faruk Gulban, Hartmut Mohlberg, Katrin Amunts, Rainer Goebel & Federico De Martino
OHBM 2019 conference poster.

Comparison between cytoarchitectonic and MRI based parcellation of the human auditory cortex

Omer Faruk Gulban, Hartmut Mohlberg, Katrin Amunts, Rainer Goebel & Federico De Martino
OHBM 2019 conference poster.

Comparison between cytoarchitectonic and MRI based parcellation of the human auditory cortex

Omer Faruk Gulban, Hartmut Mohlberg, Katrin Amunts, Rainer Goebel & Federico De Martino
OHBM 2019 conference poster.

The epg5 knockout zebrafish line: a model to study Vici syndrome

Giacomo Meneghetti, Tatjana Skobo, Martina Chrisam, Nicola Facchinello, Camilla Maria Fontana, Stefania Bellesso, Patrizia Sabatelli, Flavia Raggi, Francesco Cecconi, Paolo Bonaldo & Luisa Dalla Valle
The EPG5 protein is a RAB7A effector involved in fusion specificity between autophagosomes and late endosomes or lysosomes during macroautophagy/autophagy. Mutations in the human EPG5 gene cause a rare and severe multisystem disorder called Vici syndrome. In this work, we show that zebrafish epg5-/- mutants from both heterozygous and incrossed homozygous matings are viable and can develop to the age of sexual maturity without conspicuous defects in external appearance. In agreement with the dysfunctional autophagy...

The epg5 knockout zebrafish line: a model to study Vici syndrome

Giacomo Meneghetti, Tatjana Skobo, Martina Chrisam, Nicola Facchinello, Camilla Maria Fontana, Stefania Bellesso, Patrizia Sabatelli, Flavia Raggi, Francesco Cecconi, Paolo Bonaldo & Luisa Dalla Valle
The EPG5 protein is a RAB7A effector involved in fusion specificity between autophagosomes and late endosomes or lysosomes during macroautophagy/autophagy. Mutations in the human EPG5 gene cause a rare and severe multisystem disorder called Vici syndrome. In this work, we show that zebrafish epg5-/- mutants from both heterozygous and incrossed homozygous matings are viable and can develop to the age of sexual maturity without conspicuous defects in external appearance. In agreement with the dysfunctional autophagy...

SIRT3 promotes antimycobacterial defenses by coordinating mitochondrial and autophagic functions

Tae Sung Kim, Yeung Bae Jin, Yi Sak Kim, Sup Kim, Jin Kyung Kim, Hye-Mi Lee, Hyun-Woo Suh, Jin Ho Choe, Young Jae Kim, Bon-Sang Koo, Han-Na Kim, Mingyu Jung, Sang-Hee Lee, Don-Kyu Kim, Chaeuk Chung, Ji-Woong Son, Jung-Joon Min, Jin-Man Kim, Chu-Xia Deng, Hyun Seok Kim, Sang-Rae Lee & Eun-Kyeong Jo
SIRT3 (sirtuin 3), a mitochondrial protein deacetylase, maintains respiratory function, but its role in the regulation of innate immune defense is largely unknown. Herein, we show that SIRT3 coordinates mitochondrial function and macroautophagy/autophagy activation to promote anti-mycobacterial responses through PPARA (peroxisome proliferator activated receptor alpha). SIRT3 deficiency enhanced inflammatory responses and mitochondrial dysfunction, leading to defective host defense and pathological inflammation during mycobacterial infection. Antibody-mediated depletion of polymorphonuclear neutrophils significantly increased protection against mycobacterial infection...

SIRT3 promotes antimycobacterial defenses by coordinating mitochondrial and autophagic functions

Tae Sung Kim, Yeung Bae Jin, Yi Sak Kim, Sup Kim, Jin Kyung Kim, Hye-Mi Lee, Hyun-Woo Suh, Jin Ho Choe, Young Jae Kim, Bon-Sang Koo, Han-Na Kim, Mingyu Jung, Sang-Hee Lee, Don-Kyu Kim, Chaeuk Chung, Ji-Woong Son, Jung-Joon Min, Jin-Man Kim, Chu-Xia Deng, Hyun Seok Kim, Sang-Rae Lee & Eun-Kyeong Jo
SIRT3 (sirtuin 3), a mitochondrial protein deacetylase, maintains respiratory function, but its role in the regulation of innate immune defense is largely unknown. Herein, we show that SIRT3 coordinates mitochondrial function and macroautophagy/autophagy activation to promote anti-mycobacterial responses through PPARA (peroxisome proliferator activated receptor alpha). SIRT3 deficiency enhanced inflammatory responses and mitochondrial dysfunction, leading to defective host defense and pathological inflammation during mycobacterial infection. Antibody-mediated depletion of polymorphonuclear neutrophils significantly increased protection against mycobacterial infection...

Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function

Devdutt Sharma, Grant Otto, Eleanor Warren, Philip Beesley, Jason S. King & Robin S.B. Williams
Mutations in the g-secretase complex are strongly associated with familial Alzheimer disease. Both proteolytic and non-proteolytic functions for the γ-secretase complex have been previously described in mammalian model organisms, but their relative contributions to disease pathology remain unclear. Here, we dissect the roles of orthologs of the γ-secretase components in the model system Dictyostelium, focusing on endocytosis, lysosomal activity and autophagy. In this model, we show that the orthologs of PSEN (psenA and psenB), Ncstn...

Lysosomal inhibition attenuates peroxisomal gene transcription via suppression of PPARA and PPARGC1A levels

Hayden Weng Siong Tan, B. Anjum, Han-Ming Shen, Sujoy Ghosh, Paul M. Yen & Rohit A. Sinha
Lysosomes influence dynamic cellular processes such as nutrient sensing and transcriptional regulation. To explore novel transcriptional pathways regulated by lysosomes, we performed microarray analysis followed by qPCR validation in a mouse hepatocyte cell line, AML12, treated with bafilomycin A1 (lysosomal v-type H+-translocating ATPase inhibitor). Pathway enrichment analysis revealed significant downregulation of gene sets related to peroxisomal biogenesis and peroxisomal lipid oxidation upon lysosomal inhibition. Mechanistically, pharmacological inhibition of lysosomes as well as genetic knockdown of...

TP53INP2 contributes to autophagosome formation by promoting LC3-ATG7 interaction

Zhiyuan You, Yinfeng Xu, Wei Wan, Li Zhou, Jin Li, Tianhua Zhou, Yin Shi & Wei Liu
TP53INP2/DOR (tumor protein p53-inducible nuclear protein 2) contributes to mammalian macroautophagy/autophagy by carrying nuclear deacetylated MAP1LC3/LC3 to the cytoplasm. Here, we report that in the cytoplasm, TP53INP2 further functions in autophagosome biogenesis by promoting LC3B-ATG7 interaction. Cytoplasmic expression of the N-terminal region of TP53INP2, which includes the LC3-interacting region, effectively triggered LC3B–PE production and autophagosome formation. In the cytoplasm, TP53INP2 colocalized to early autophagic membrane structures containing ATG14, ZFYVE1/DFCP1 or WIPI2. While knockdown of TP53INP2...

Lysosomal inhibition attenuates peroxisomal gene transcription via suppression of PPARA and PPARGC1A levels

Hayden Weng Siong Tan, B. Anjum, Han-Ming Shen, Sujoy Ghosh, Paul M. Yen & Rohit A. Sinha
Lysosomes influence dynamic cellular processes such as nutrient sensing and transcriptional regulation. To explore novel transcriptional pathways regulated by lysosomes, we performed microarray analysis followed by qPCR validation in a mouse hepatocyte cell line, AML12, treated with bafilomycin A1 (lysosomal v-type H+-translocating ATPase inhibitor). Pathway enrichment analysis revealed significant downregulation of gene sets related to peroxisomal biogenesis and peroxisomal lipid oxidation upon lysosomal inhibition. Mechanistically, pharmacological inhibition of lysosomes as well as genetic knockdown of...

TP53INP2 contributes to autophagosome formation by promoting LC3-ATG7 interaction

Zhiyuan You, Yinfeng Xu, Wei Wan, Li Zhou, Jin Li, Tianhua Zhou, Yin Shi & Wei Liu
TP53INP2/DOR (tumor protein p53-inducible nuclear protein 2) contributes to mammalian macroautophagy/autophagy by carrying nuclear deacetylated MAP1LC3/LC3 to the cytoplasm. Here, we report that in the cytoplasm, TP53INP2 further functions in autophagosome biogenesis by promoting LC3B-ATG7 interaction. Cytoplasmic expression of the N-terminal region of TP53INP2, which includes the LC3-interacting region, effectively triggered LC3B–PE production and autophagosome formation. In the cytoplasm, TP53INP2 colocalized to early autophagic membrane structures containing ATG14, ZFYVE1/DFCP1 or WIPI2. While knockdown of TP53INP2...

Radiation induces EIF2AK3/PERK and ERN1/IRE1 mediated pro-survival autophagy

Madhuri Chaurasia, Swapnil Gupta, Asmita Das, B.S. Dwarakanath, Anne Simonsen & Kulbhushan Sharma
Cellular effects of ionizing radiation include oxidative damage to macromolecules, unfolded protein response (UPR) and metabolic imbalances. Oxidative stress and UPR have been shown to induce macroautophagy/autophagy in a context-dependent manner and are crucial factors in determining the fate of irradiated cells. However, an in-depth analysis of the relationship between radiation-induced damage and autophagy has not been explored. In the present study, we investigated the relationship between radiation-induced oxidative stress, UPR and autophagy in murine...

Radiation induces EIF2AK3/PERK and ERN1/IRE1 mediated pro-survival autophagy

Madhuri Chaurasia, Swapnil Gupta, Asmita Das, B.S. Dwarakanath, Anne Simonsen & Kulbhushan Sharma
Cellular effects of ionizing radiation include oxidative damage to macromolecules, unfolded protein response (UPR) and metabolic imbalances. Oxidative stress and UPR have been shown to induce macroautophagy/autophagy in a context-dependent manner and are crucial factors in determining the fate of irradiated cells. However, an in-depth analysis of the relationship between radiation-induced damage and autophagy has not been explored. In the present study, we investigated the relationship between radiation-induced oxidative stress, UPR and autophagy in murine...

A novel transgenic zebrafish line allows for in vivo quantification of autophagic activity in neurons

Sataree Khuansuwan, Lisa M. Barnhill, Sizhu Cheng & Jeff M. Bronstein
The pathophysiology of most neurodegenerative diseases includes aberrant accumulation of protein aggregates. Recent evidence highlights the role of protein degradation pathways in neurodegeneration. Concurrently, genetic tools have been generated to enable zebrafish, Danio rerio, to be used as an animal model to study neurodegenerative processes. In addition to optical clarity and fast ex utero development, the zebrafish brain is relatively small and has conserved structures with its mammalian counterparts. To take advantage of this model...

Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function

Devdutt Sharma, Grant Otto, Eleanor C. Warren, Philip Beesley, Jason S. King & Robin S. B. Williams
Mutations in the γ-secretase complex are strongly associated with familial Alzheimer disease. Both proteolytic and non-proteolytic functions for the γ-secretase complex have been previously described in mammalian model organisms, but their relative contributions to disease pathology remain unclear. Here, we dissect the roles of orthologs of the γ-secretase components in the model system Dictyostelium, focusing on endocytosis, lysosomal activity and autophagy. In this model, we show that the orthologs of PSEN (psenA and psenB), Ncstn...

A novel transgenic zebrafish line allows for in vivo quantification of autophagic activity in neurons

Sataree Khuansuwan, Lisa M. Barnhill, Sizhu Cheng & Jeff M. Bronstein
The pathophysiology of most neurodegenerative diseases includes aberrant accumulation of protein aggregates. Recent evidence highlights the role of protein degradation pathways in neurodegeneration. Concurrently, genetic tools have been generated to enable zebrafish, Danio rerio, to be used as an animal model to study neurodegenerative processes. In addition to optical clarity and fast ex utero development, the zebrafish brain is relatively small and has conserved structures with its mammalian counterparts. To take advantage of this model...

Gamma secretase orthologs are required for lysosomal activity and autophagic degradation in Dictyostelium discoideum, independent of PSEN (presenilin) proteolytic function

Devdutt Sharma, Grant Otto, Eleanor C. Warren, Philip Beesley, Jason S. King & Robin S. B. Williams
Mutations in the γ-secretase complex are strongly associated with familial Alzheimer disease. Both proteolytic and non-proteolytic functions for the γ-secretase complex have been previously described in mammalian model organisms, but their relative contributions to disease pathology remain unclear. Here, we dissect the roles of orthologs of the γ-secretase components in the model system Dictyostelium, focusing on endocytosis, lysosomal activity and autophagy. In this model, we show that the orthologs of PSEN (psenA and psenB), Ncstn...

RADIATION INDUCES EIF2AK3/PERK AND ERN1/IRE1 MEDIATED PRO-SURVIVAL AUTOPHAGY

Madhuri Chaurasia, Swapnil Gupta, Asmita Das, B.S. Dwarakanath, Anne Simonsen & Kulbhushan Sharma
Cellular effects of ionizing radiation include oxidative damage to macromolecules, unfolded protein response (UPR) and metabolic imbalances. Oxidative stress and UPR have been shown to induce macroautophagy/autophagy in a context-dependent manner and are crucial factors in determining the fate of irradiated cells. However, an in-depth analysis of the relationship between radiation-induced damage and autophagy has not been explored. In the present study, we investigated the relationship between radiation-induced oxidative stress, UPR and autophagy in murine...

A novel transgenic zebrafish line allows for in vivo quantification of autophagic activity in neurons

Sataree Khuansuwan, Lisa M. Barnhill, Sizhu Cheng & Jeff M. Bronstein
The pathophysiology of most neurodegenerative diseases includes aberrant accumulation of protein aggregates. Recent evidence highlights the role of protein degradation pathways in neurodegeneration. Concurrently, genetic tools have been generated to enable zebrafish, Danio rerio, to be used as an animal model to study neurodegenerative processes. In addition to optical clarity and fast ex utero development, the zebrafish brain is relatively small and has conserved structures with its mammalian counterparts. To take advantage of this model...

Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs

Åsa Birna Birgisdottir, Stephane Mouilleron, Zambarlal Bhujabal, Martina Wirth, Eva Sjøttem, Gry Evjen, Wenxin Zhang, Rebecca Lee, Nicola O’Reilly, Sharon A. Tooze, Trond Lamark & Terje Johansen
Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 and ATG14 and phosphorylates phosphatidylinositol to generate phosphatidylinositol 3-phosphate (PtdIns3P). Here, we show that PIK3C3, BECN1 and ATG14 contain functional LIR motifs and interact with the Atg8-family proteins with...

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