scholarly journals Using Nanobodies to Study Protein Function in Developing Organisms

Antibodies ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 16 ◽  
Author(s):  
Gustavo Aguilar ◽  
Shinya Matsuda ◽  
M. Alessandra Vigano ◽  
Markus Affolter
Keyword(s):  
Developmental Biology ◽  
Protein Function ◽  
Dependent Manner ◽  
Single Chain ◽  
Functional Studies ◽  
Extracellular Milieu ◽  
The Past ◽  
Biological Studies ◽  
Living Organisms

Polyclonal and monoclonal antibodies have been invaluable tools to study proteins over the past decades. While indispensable for most biological studies including developmental biology, antibodies have been used mostly in fixed tissues or as binding reagents in the extracellular milieu. For functional studies and for clinical applications, antibodies have been functionalized by covalently fusing them to heterologous partners (i.e., chemicals, proteins or other moieties). Such functionalized antibodies have been less widely used in developmental biology studies. In the past few years, the discovery and application of small functional binding fragments derived from single-chain antibodies, so-called nanobodies, has resulted in novel approaches to study proteins during the development of multicellular animals in vivo. Expression of functionalized nanobody fusions from integrated transgenes allows manipulating proteins of interest in the extracellular and the intracellular milieu in a tissue- and time-dependent manner in an unprecedented manner. Here, we describe how nanobodies have been used in the field of developmental biology and look into the future to imagine how else nanobody-based reagents could be further developed to study the proteome in living organisms.

scholarly journals Peptidic degron for IMiD-induced degradation of heterologous proteins

2019 ◽  
Vol 116 (7) ◽  
pp. 2539-2544 ◽  
Author(s):  
Vidyasagar Koduri ◽  
Samuel K. McBrayer ◽  
Ella Liberzon ◽  
Adam C. Wang ◽  
Kimberly J. Briggs ◽  
...  
Keyword(s):  
Protein Function ◽  
Cultured Cells ◽  
Ex Vivo ◽  
Ease Of Use ◽  
Dependent Manner ◽  
Heterologous Proteins ◽  
Ubiquitin Ligase Complex ◽  
Dose Dependent ◽  
Current Systems

Current systems for modulating the abundance of proteins of interest in living cells are powerful tools for studying protein function but differ in terms of their complexity and ease of use. Moreover, no one system is ideal for all applications, and the best system for a given protein of interest must often be determined empirically. The thalidomide-like molecules (collectively called the IMiDs) bind to the ubiquitously expressed cereblon ubiquitin ligase complex and alter its substrate specificity such that it targets the IKZF1 and IKZF3 lymphocyte transcription factors for destruction. Here, we mapped the minimal IMiD-responsive IKZF3 degron and show that this peptidic degron can be used to target heterologous proteins for destruction with IMiDs in a time- and dose-dependent manner in cultured cells grown ex vivo or in vivo.

Cements: Reactor Response

1988 ◽  
Vol 2 (1) ◽  
pp. 145-149
Author(s):  
M.D. Jendresen
Keyword(s):  
Major Change ◽  
Organic Films ◽  
Research Needs ◽  
Compositional Change ◽  
Research Teams ◽  
Dental Cement ◽  
The Past ◽  
Living Organisms ◽  
Biological Environment

Many of the dental cement research needs for the future should be related to the biological environment, organic films, living organisms, and experimentation in vivo. Research in these areas will create new opportunities for physical scientists to collaborate with biological scientists, establishing research teams with composition quite different from those in the past. That compositional change could be the major change in dental cement research for the balance of the 1980's.

scholarly journals SET7/9-dependent methylation of ARTD1 at K508 stimulates poly-ADP-ribose formation after oxidative stress

Open Biology ◽  
2013 ◽  
Vol 3 (10) ◽  
pp. 120173 ◽  
Author(s):  
Ingrid Kassner ◽  
Anneli Andersson ◽  
Monika Fey ◽  
Martin Tomas ◽  
Elisa Ferrando-May ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Protein Interactions ◽  
Protein Function ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Target Proteins ◽  
Protein Methyltransferase

ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1, formerly PARP1) is localized in the nucleus, where it ADP-ribosylates specific target proteins. The post-translational modification (PTM) with a single ADP-ribose unit or with polymeric ADP-ribose (PAR) chains regulates protein function as well as protein–protein interactions and is implicated in many biological processes and diseases. SET7/9 (Setd7, KMT7) is a protein methyltransferase that catalyses lysine monomethylation of histones, but also methylates many non-histone target proteins such as p53 or DNMT1. Here, we identify ARTD1 as a new SET7/9 target protein that is methylated at K508 in vitro and in vivo . ARTD1 auto-modification inhibits its methylation by SET7/9, while auto-poly-ADP-ribosylation is not impaired by prior methylation of ARTD1. Moreover, ARTD1 methylation by SET7/9 enhances the synthesis of PAR upon oxidative stress in vivo . Furthermore, laser irradiation-induced PAR formation and ARTD1 recruitment to sites of DNA damage in a SET7/9-dependent manner. Together, these results reveal a novel mechanism for the regulation of cellular ARTD1 activity by SET7/9 to assure efficient PAR formation upon cellular stress.

scholarly journals The vacuolar kinase Yck3 maintains organelle fragmentation by regulating the HOPS tethering complex

2005 ◽  
Vol 168 (3) ◽  
pp. 401-414 ◽  
Author(s):  
Tracy J. LaGrassa ◽  
Christian Ungermann
Keyword(s):  
Cellular Membrane ◽  
Membrane Dynamics ◽  
Dependent Manner ◽  
Casein Kinase I ◽  
Functional Protein ◽  
Hypertonic Stress ◽  
Functional Studies ◽  
Vacuole Fusion

The regulation of cellular membrane flux is poorly understood. Yeast respond to hypertonic stress by fragmentation of the normally large, low copy vacuole. We used this phenomenon as the basis for an in vivo screen to identify regulators of vacuole membrane dynamics. We report here that maintenance of the fragmented phenotype requires the vacuolar casein kinase I Yck3: when Yck3 is absent, salt-stressed vacuoles undergo fission, but reassemble in a SNARE-dependent manner, suggesting that vacuole fusion is disregulated. Accordingly, when Yck3 is deleted, in vitro vacuole fusion is increased, and Yck3 overexpression blocks fusion. Morphological and functional studies show that Yck3 modulates the Rab/homotypic fusion and vacuole protein sorting complex (HOPS)-dependent tethering stage of vacuole fusion. Intriguingly, Yck3 mediates phosphorylation of the HOPS subunit Vps41, a bi-functional protein involved in both budding and fusion during vacuole biogenesis. Because Yck3 also promotes efficient vacuole inheritance, we propose that tethering complex phosphorylation is a part of a general, switch-like mechanism for driving changes in organelle architecture.

Recombinant Rat Protein C: Comparative Studies of Structure, Function and Synthesis with Plasma Protein C

1994 ◽  
Vol 71 (01) ◽  
pp. 054-061 ◽  
Author(s):  
Mayumi Ono ◽  
Hiroyuki Fujiwara ◽  
Takaaki Okafuji ◽  
Tomoko Enjoh ◽  
Katsuhiko Nawa
Keyword(s):  
Heavy Chain ◽  
Light Chain ◽  
Protein C ◽  
Rat Hepatocytes ◽  
Rat Plasma ◽  
Chain Molecule ◽  
Dependent Manner ◽  
Single Chain

SummaryIn order to elucidate the role of protein C (PC) in the rat, we expressed, purified, and characterized recombinant rat PC. The purified recombinant rat PC was 70–90% two-chain (41 kDa heavy chain; 22 and 23 kDa light chain) and 10–30% single-chain (61 kDa). Amino acid analysis confirmed the presence of 10 moles of γ-carboxyglutamic acid residues per mol of protein. For comparison, plasma rat PC was purified from a barium citrate precipitate using similar method. Plasma rat PC was a two-chain form (41 kDa heavy chain; 22 kDa light chain) with no detectable single-chain nor 23 kDa light chain. For determination of the in vitro secreted species, primary cultured rat hepatocytes were incubated for 6 h with methionine-free MEM containing vitamin K1, aprotinin, and [35S]methionine. The supernatant was immunoprecipitated and analyzed by SDS-PAGE followed by autoradiography. Approximately 90% of the PC radioactivity migrated as a two-chain molecule. These results indicate that rat PC is secreted mainly as a two-chain molecule from the liver. PROTAC-activated forms of recombinant rat PC, plasma rat PC, and plasma human PC hydrolyzed the S-2366 chromogenic substrate at the same rate Recombinant rat PC was also activated by the thrombin-thrombomodulin complex at a rate similar to plasma lat PC. The anticoagulant activities of the three activated PCs were examined in rat plasma. Both recombinant and plasma rat PC prolonged the activated partial thromboplastin time in a dose-dependent manner, but plasma human PC was less effective. These results suggest that recombinant rat PC is applicable for in vivo thrombosis studies in the rat.

scholarly journals Biologically active recombinant carp LH as a spawning-inducing agent for carp

2017 ◽  
Vol 232 (3) ◽  
pp. 391-402 ◽  
Author(s):  
Joseph Aizen ◽  
Lian Hollander-Cohen ◽  
Michal Shpilman ◽  
Berta Levavi-Sivan
Keyword(s):  
Large Scale ◽  
Biological Response ◽  
Biologically Active ◽  
Dopamine Antagonist ◽  
Dependent Manner ◽  
Single Chain ◽  
Terminal Part ◽  
Α Subunit ◽  
Subsequent Decrease

Currently, spawning is induced in carp species by carp pituitary extract (CPE) and a combination of synthetic agonist of GnRH combined with a dopamine antagonist. The main goal of this study was the production of recombinant gonadotropins (GtHs) on a large scale to serve as an alternative to currently used agents. We produced carp (c) recombinant (r) Lh as a single chain in the methylotrophic yeast Pichia pastoris. Lha subunit was joined with Lhb subunit with a flexible linker of three glycine–serine repeats and six Histidines to form a mature protein, the β-subunit formed the N-terminal part and the α-subunit formed the C-terminal part. The ability of the rcLh to elicit biological response was tested by in vivo stimulation of estradiol (E2) and 17α,20β-dihydroxy-4-pregnen-3-one (DHP) and by its in vivo potency to induce ovulation and spawning induction. rcLh tested in this work significantly enhanced both E2 and DHP secretion in a dose-dependent manner similar to the results obtained with CPE. E2 levels showed a moderate rise following the priming injection and a subsequent decrease during the rest of the trial. DHP levels were only increased after the resolving injection, approximately 5 h before spawning. At the highest dose of rcLh (350 µg/kg BW), the recombinant protein was more efficient than CPE in terms of both spawning success and fertilization rate. It is shown here that rcLh can elicit the secretion of DHP in vivo and actually trigger spawning. These novel findings introduce the potential of utilizing recombinant gonadotropins in aquaculture.

scholarly journals TRIM39 deficiency inhibits tumor progression and autophagic flux in colorectal cancer via suppressing the activity of Rab7

2021 ◽  
Vol 12 (4) ◽  
Author(s):  
Jia Hu ◽  
Xueliang Ding ◽  
Shaobo Tian ◽  
Yanan Chu ◽  
Zhibo Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Autophagic Flux ◽  
Dependent Manner ◽  
Functional Studies ◽  
Normal Tissues ◽  
Tumor Tissues ◽  
Autophagic Degradation ◽  
Activity Dependent

AbstractThe biological function of TRIM39, a member of TRIM family, remains largely unexplored in cancer, especially in colorectal cancer (CRC). In this study, we show that TRIM39 is upregulated in tumor tissues compared to adjacent normal tissues and associated with poor prognosis in CRC. Functional studies demonstrate that TRIM39 deficiency restrains CRC progression in vitro and in vivo. Our results further find that TRIM39 is a positive regulator of autophagosome–lysosome fusion. Mechanistically, TRIM39 interacts with Rab7 and promotes its activity via inhibiting its ubiquitination at lysine 191 residue. Depletion of TRIM39 inhibits CRC progression and autophagic flux in a Rab7 activity-dependent manner. Moreover, TRIM39 deficiency suppresses CRC progression through inhibiting autophagic degradation of p53. Thus, our findings uncover the roles as well as the relevant mechanisms of TRIM39 in CRC and establish a functional relationship between autophagy and CRC progression, which may provide promising approaches for the treatment of CRC.

scholarly journals Upregulated of TBX1 by genetic variants are associated with human congenital heart disease

2021 ◽  
Author(s):  
Liwei Yu ◽  
Binbin Li ◽  
Hongyan Wang
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
Genetic Variants ◽  
Protein Function ◽  
Congenital Heart ◽  
Protein S ◽  
Dependent Manner ◽  
Functional Studies ◽  
Childhood Morbidity ◽  
Chd Risk

Congenital heart disease (CHD) is the most common human birth defect worldwide and also an important cause of childhood morbidity and mortality. The transcription factor of TBX1 early expressed in embryonic cardiac progenitor cells underlys embryo cardiogenesis in a dosage-dependent manner. Imbalanced TBX1 level has been shown to lead to cardiac defects. To study the association of TBX1 genetic variants with CHD susceptibility, we screened genetic variants in 409 CHD patients and 203 healthy controls. One single nucleotide polymorphism (SNP), rs41260844, in TBX1 promotor region was identified to be associated with CHD. Functional studies showed the minor allele of rs41260844 is associated with higher CHD risk and increases TBX1 promoter activity through attenuating TBX1 promoter binding affinity with nuclear protein(s). In addition, a novel case-specific missense rare mutation of p.P164L in TBX1 T-box domain was identified and predicted as deleterious mutation, which showed a trend of increased protein function. In summary, we concluded that a higher TBX1 expression level or activity is associated with CHD susceptibility, which could affect TBX1 downstream targets and thus disrupt the balance of the complex regulation network during cardiogenesis. This study deepens our current understanding of embryo cardiogenesis and CHD etiology.

scholarly journals Behavioral phenotyping of Zip8 393T-KI mice for in vivo study of schizophrenia pathogenesis

2021 ◽  
Author(s):  
Chantelle E Terrillion ◽  
Byung-hak Kang ◽  
Joanna MP Melia
Keyword(s):  
Protein Function ◽  
Field Testing ◽  
Genetic Associations ◽  
Behavioral Differences ◽  
Behavioral Phenotyping ◽  
Functional Studies ◽  
Y Maze ◽  
Genetic Landscape ◽  
Trace Fear

Genetic studies have informed on the genetic landscape of schizophrenia, and the next challenge is to link the genetic associations to mechanistic studies. A common single nucleotide polymorphism in the zinc and manganese transporter ZIP8 (rs13107325; ZIP8 A391T) is a top candidate to prioritize for functional studies because it is a missense mutation that results in hypomorphic protein function. With this goal, we have established a mouse model (Zip8 393T-knock-in (KI)), and here, we report the results of brain necropsy and initial behavioral phenotyping experiments in the KI mice using open field testing, elevated plus maze, Y-maze, and trace fear conditioning. Overall, male, homozygous KI mice may exhibit subtle defects in cognition and spatial learning, otherwise the baseline testing supports minimal behavioral differences between wild-type and Zip8 393T-KI mice. There were no genotype-specific alterations of gross or microscopic neuroanatomy. These experiments are important to establish the baseline characteristics of the Zip8 393T-KI mice that may be perturbed in animal models of schizophrenia and position the Zip8 393T-KI mouse as an important model for translational studies of schizophrenia pathogenesis.

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