Multiple shoot induction and plant regeneration in litchi (Litchi chinensis Sonn.)

Multiple shoot induction in Litchi chinensis Sonn. (litchi) has been achieved by two methods: (1) direct germination of litchi seeds in 6-benzylaminopurine (20 mg l^–1)-supplemented MS liquid medium and supported on a filter-paper bridge and (2) in planta treatment with 6-benzylaminopurine (100 μg on alternate days) of the axillary bud regions of plants germinated and maintained under sterile conditions. While the former method resulted in as many as 27.5±8.6 shoot buds from the cotyledonary node within 4 weeks, the latter yielded on average approximately 8 shoot buds from each treated node in 8 weeks. The cytokinin treatment in planta consisted of placing sterile filter paper moistened with sterile distilled water over the node and adding different concentrations of 6-benzylaminopurine. Both methods of multiple shoot induction were found to be effective for the five genotypes of litchi that were tested. The shoots elongated and rooted directly in vermiculite after a pulse treatment with IBA (25 mg/ml) for 15 min. Fungus growth which is a serious problem in litchi tissue culture, was controlled using a fungicide, Bavistin, and by eliminating organic nutrients from the growth medium. Received: 27 July 1998 / Revision received: 30 September 1998 / Accepted: 27 October 1998     

A network map of apelin-mediated signaling

The apelin receptor (APLNR) is a class A (rhodopsin-like) G-protein coupled receptor with a wide distribution throughout the human body. Activation of the apelin/APLNR system regulates AMPK/PI3K/AKT/mTOR and RAF/ERK1/2 mediated signaling pathways. APLNR activation orchestrates several downstream signaling cascades, which play diverse roles in physiological effects, including effects upon vasoconstriction, heart muscle contractility, energy metabolism regulation, and fluid homeostasis angiogenesis. We consolidated a network map of the APLNR signaling map owing to its biomedical importance. The curation of literature data pertaining to the APLNR system was performed manually by the NetPath criteria. The described apelin receptor signaling map comprises 35 activation/inhibition events, 38 catalysis events, 4 molecular associations, 62 gene regulation events, 113 protein expression types, and 4 protein translocation events. The APLNR signaling pathway map data is made freely accessible through the WikiPathways Database (https://www.wikipathways.org/index.php/Pathway:WP5067).Supplementary InformationThe online version contains supplementary material available at 10.1007/s12079-021-00614-6.     

Trophic factor BDNF inhibits GABAergic signaling by facilitating dendritic enrichment of SUMO E3 ligase PIAS3 and altering gephyrin scaffold

Posttranslational addition of a small ubiquitin-like modifier (SUMO) moiety (SUMOylation) has been implicated in pathologies such as brain ischemia, diabetic peripheral neuropathy, and neurodegeneration. However, nuclear enrichment of SUMO pathway proteins has made it difficult to ascertain how ion channels, proteins that are typically localized to and function at the plasma membrane, and mitochondria are SUMOylated. Here, we report that the trophic factor, brain-derived neurotrophic factor (BDNF) regulates SUMO proteins both spatially and temporally in neurons. We show that BDNF signaling via the receptor tropomyosin-related kinase B facilitates nuclear exodus of SUMO proteins and subsequent enrichment within dendrites. Of the various SUMO E3 ligases, we found that PIAS-3 dendrite enrichment in response to BDNF signaling specifically modulates subsequent ERK1/2 kinase pathway signaling. In addition, we found the PIAS-3 RING and Ser/Thr domains, albeit in opposing manners, functionally inhibit GABA-mediated inhibition. Finally, using oxygen–glucose deprivation as an in vitro model for ischemia, we show that BDNF–tropomyosin-related kinase B signaling negatively impairs clustering of the main scaffolding protein at GABAergic postsynapse, gephyrin, whereby reducing GABAergic neurotransmission postischemia. SUMOylation-defective gephyrin K148R/K724R mutant transgene expression reversed these ischemia-induced changes in gephyrin cluster density. Taken together, these data suggest that BDNF signaling facilitates the temporal relocation of nuclear-enriched SUMO proteins to dendrites to influence postsynaptic protein SUMOylation.     

Neurobiology of echolocation in bats

Echolocating bats (sub-order: Microchiroptera) form a highly successful group of animals, comprising approximately 700 species and an estimated 25% of living mammals. Many echolocating bats are nocturnal predators that have evolved a biological sonar system to orient and forage in three-dimensional space. Acoustic signal processing and vocal-motor control are tightly coupled, and successful echolocation depends on the coordination between auditory and motor systems. Indeed, echolocation involves adaptive changes in vocal production patterns, which, in turn, constrain the acoustic information arriving at the bat's ears and the time-scales over which neural computations take place.     

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis

Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.     

Biotransformation of ferulic acid to acetovanillone using Rhizopus oryzae

Microbial transformation of ferulic acid to acetovanillone was studied using growing cells of Rhizopus oryzae. Ferulic acid was added to the growing medium (0.5 g L^-1) and incubated for 12 days. The progress of formation of metabolites was monitored by GC and GC-MS after extraction with ethyl acetate. The major metabolite was acetovanillone with minor metabolites formed, such as dihydroferulic acid, coniferyl alcohol and dihydroconiferyl alcohol. Traces of metabolites (≤1-3%), such as vanillin, vanillyl alcohol, vanillic acid and phenyl ethyl alcohol, were also produced. Formation of 4-vinyl guaiacol increased from day 1 (12.4%), reaching a maximum on day 4 (31.7%), and reducing to a minimum on day 12 (3.1%). The formation of acetovanillone increased only from day 2 onward, and reached a maximum (49.2%) on day 12. The optimum concentration of ferulic acid to be added into the medium was found to be only 0.5 g L^-1, as any increase in concentration (0.75 and 1.0 g L^-1) precipitated the precursor, resulting in no further degradation.     

Expressions of pathologic markers in PRP based chondrogenic differentiation of human adipose derived stem cells

Background

Optimization of the differentiation medium through using autologous factors such as PRP is of great consideration, but due to the complex, variable and undefined composition of PRP on one hand and lack of control over the absolute regulatory mechanisms in in vitro conditions or disrupted and different mechanisms in diseased tissue microenvironments in in vivo conditions on the other hand, it is complicated and rather unpredictable to get the desired effects of PRP making it inevitable to monitor the possible pathologic or undesired differentiation pathways and therapeutic effects of PRP. Therefore, in this study the probable potential of PRP on inducing calcification, inflammation and angiogenesis in chondrogenically-differentiated cells was investigated.

A computational workflow for predicting cancer neo-antigens

Neo-antigens presented on cell surface play a pivotal role in the success of immunotherapies. Peptides derived from mutant proteins are thought to be the primary source of neo-antigens presented on the surface of cancer cells. Mutation data from cancer genome sequencing is often used to predict cancer neo-antigens. However, this strategy is associated with significant false positives as many coding mutations may not be expressed at the protein level. Hence, we describe a computational workflow to integrate genomic and proteomic data to predictpotential neo-antigens.     

The Neuroprotective Effect of Curcumin Against Nicotine-Induced Neurotoxicity is Mediated by CREB–BDNF Signaling Pathway

Neurochemical Research - Nicotine abuse adversely affects brain and causes apoptotic neurodegeneration. Curcumin- a bright yellow chemical compound found in turmeric is associated with...