YspB is a major translocator protein of Yersinia secretion apparatus- Yersinia secretion protein (Ysa-Ysp) Type III Secretion System (T3SS) of Yersinia enterocolitica Biovar 1B. SycB is the cognate class II chaperone of YspB. YspB is a highly alpha helical protein. It shows significant homology to IpaB-SipB family of proteins. YspB possesses transmembrane helices, intramolecular coiled-coil regions and intrinsically disordered regions, all characteristics of translocator proteins. Homology model of YspB showed an all helical structure interspersed by coiled regions. YspB has a star shaped three dimensional structure with five distinct arms. The first two Tetratricopeptide Repeat (TPR) regions of SycB are responsible for its interaction with YspB. The helices and the loops of YspB interacting with SycB exhibit evolutionary conservation. Besides this, some structurally conserved amino acid residues were also observed in other helices and loops of YspB. The nature of residues involved in the YspB-SycB interaction indicate towards an ionic or polar interaction between the two proteins. This model of translocator-chaperone interaction might prove to be potentially beneficial in understanding the regulation of Ysa-Ysp T3SS.
Assignment 6BIO 151 Summer 2016Upload by Friday, June 24t.docxrock73
Assignment 6 BIO 151 Summer 2016
Upload by Friday, June 24th at 12:00 PM
CHAPTER 11: CELL COMMUNICATION
1. Define the 3 stages of cell signaling:
1) Reception –
2) Transduction –
3) Response –
2. Explain the two main types of direct contact (the 1st type has different name for plants/animals; 2nd type is just found in animals – see Fig11.4):
1) Plants:
Animals:
2) Animals:
3. What is local signaling? What is an example of this?
4. What are hormones? What type of signaling are they involved in?
5. Define: Ligand –
Target cell –
6. Are signal receptors general (will they bind a variety of different signals) or are they very specific?
7. Where are intracellular receptors found?
What types of molecules bind to intracellular receptors? Why must these signals have those characteristics?
8. When a cell surface receptor receives a signal, what generally happens to the receptor? Use the ion-gated receptors as an example.
9. What is a signal transduction pathway?
Having multiple steps in the pathway provides what two things?
What are relay molecules?
Is the actual original signal passed along the pathway?
10. What are second messengers? Where do they function?
The two most common second messengers are:
1) 2)
11. Is the calcium ion concentration higher inside or outside the cell? Why? (What does the cell do to create this gradient?)
12. If the final activated molecule in a signal transduction pathway is a
__________________________________________, then the response is turning genes on or off.
13. If hormones are spread all around the body in the bloodstream, then why do only certain cell types respond to certain hormones?
CHAPTER 19: VIRUSES
1.Why are viruses generally not considered to be living organisms?
2. What is the general structure of a virus? What is a capsid?
3. Viruses are classified by their type of genetic material. (See Table 19.1) What are the different forms of genetic material that viruses can have?
4. Phages infect what type of host? Draw/depict a simple phage.
5. What does it mean that viruses have a host range?
6. Some viral infections (such as polio) cause permanent cell damage, while others (such as colds) do not. What determines this difference?
7. What does it mean that viruses are obligate intracellular parasites? What things does the host cell provide for the virus to reproduce?
8. Why can’t RNA viruses use the cell’s enzymes to replicate their viral RNA? So what else do these viruses have to bring into the host cell?
9. Why can HIV not be cured? What type of human cells does HIV infect?
What is a retrovirus?
What is reverse transcriptase?
10. What are restriction enzymes and what type of organism has these as defense against viruses?
11. Do antibiotics kill viruses?
12. What is an emerging virus?
Where do emerging viruses come from ...
According to current human opinion and knowledge living organisms can be divided into seven kingdoms. The similarities and differences between these seven groups also the relationships between them are very interesting. These relationships lead to creation the different kinds of biological terms such as, mutualism, commensalism and parasitism. So plants and animal also microorganisms have to fight sometimes. The mechanisms of pathogenicity and the mechanisms of defense can be either similar or different. Emphasizing aspect of pathogenicity of some microorganisms, such as Salmonella, Fusarium and Tobacco mosaic virus can case to disease in plants and animals.
YspB is a major translocator protein of Yersinia secretion apparatus- Yersinia secretion protein (Ysa-Ysp) Type III Secretion System (T3SS) of Yersinia enterocolitica Biovar 1B. SycB is the cognate class II chaperone of YspB. YspB is a highly alpha helical protein. It shows significant homology to IpaB-SipB family of proteins. YspB possesses transmembrane helices, intramolecular coiled-coil regions and intrinsically disordered regions, all characteristics of translocator proteins. Homology model of YspB showed an all helical structure interspersed by coiled regions. YspB has a star shaped three dimensional structure with five distinct arms. The first two Tetratricopeptide Repeat (TPR) regions of SycB are responsible for its interaction with YspB. The helices and the loops of YspB interacting with SycB exhibit evolutionary conservation. Besides this, some structurally conserved amino acid residues were also observed in other helices and loops of YspB. The nature of residues involved in the YspB-SycB interaction indicate towards an ionic or polar interaction between the two proteins. This model of translocator-chaperone interaction might prove to be potentially beneficial in understanding the regulation of Ysa-Ysp T3SS.
Assignment 6BIO 151 Summer 2016Upload by Friday, June 24t.docxrock73
Assignment 6 BIO 151 Summer 2016
Upload by Friday, June 24th at 12:00 PM
CHAPTER 11: CELL COMMUNICATION
1. Define the 3 stages of cell signaling:
1) Reception –
2) Transduction –
3) Response –
2. Explain the two main types of direct contact (the 1st type has different name for plants/animals; 2nd type is just found in animals – see Fig11.4):
1) Plants:
Animals:
2) Animals:
3. What is local signaling? What is an example of this?
4. What are hormones? What type of signaling are they involved in?
5. Define: Ligand –
Target cell –
6. Are signal receptors general (will they bind a variety of different signals) or are they very specific?
7. Where are intracellular receptors found?
What types of molecules bind to intracellular receptors? Why must these signals have those characteristics?
8. When a cell surface receptor receives a signal, what generally happens to the receptor? Use the ion-gated receptors as an example.
9. What is a signal transduction pathway?
Having multiple steps in the pathway provides what two things?
What are relay molecules?
Is the actual original signal passed along the pathway?
10. What are second messengers? Where do they function?
The two most common second messengers are:
1) 2)
11. Is the calcium ion concentration higher inside or outside the cell? Why? (What does the cell do to create this gradient?)
12. If the final activated molecule in a signal transduction pathway is a
__________________________________________, then the response is turning genes on or off.
13. If hormones are spread all around the body in the bloodstream, then why do only certain cell types respond to certain hormones?
CHAPTER 19: VIRUSES
1.Why are viruses generally not considered to be living organisms?
2. What is the general structure of a virus? What is a capsid?
3. Viruses are classified by their type of genetic material. (See Table 19.1) What are the different forms of genetic material that viruses can have?
4. Phages infect what type of host? Draw/depict a simple phage.
5. What does it mean that viruses have a host range?
6. Some viral infections (such as polio) cause permanent cell damage, while others (such as colds) do not. What determines this difference?
7. What does it mean that viruses are obligate intracellular parasites? What things does the host cell provide for the virus to reproduce?
8. Why can’t RNA viruses use the cell’s enzymes to replicate their viral RNA? So what else do these viruses have to bring into the host cell?
9. Why can HIV not be cured? What type of human cells does HIV infect?
What is a retrovirus?
What is reverse transcriptase?
10. What are restriction enzymes and what type of organism has these as defense against viruses?
11. Do antibiotics kill viruses?
12. What is an emerging virus?
Where do emerging viruses come from ...
According to current human opinion and knowledge living organisms can be divided into seven kingdoms. The similarities and differences between these seven groups also the relationships between them are very interesting. These relationships lead to creation the different kinds of biological terms such as, mutualism, commensalism and parasitism. So plants and animal also microorganisms have to fight sometimes. The mechanisms of pathogenicity and the mechanisms of defense can be either similar or different. Emphasizing aspect of pathogenicity of some microorganisms, such as Salmonella, Fusarium and Tobacco mosaic virus can case to disease in plants and animals.
this is a review about evolution of antibiotic resistance. I tried to answer how bacteria acquire new genes to resist, how they choose, what are people doing to prevent this increasing resistance levels.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
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Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
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optics at visible wavelengths.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
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Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
ISI 2024: Application Form (Extended), Exam Date (Out), EligibilitySciAstra
The Indian Statistical Institute (ISI) has extended its application deadline for 2024 admissions to April 2. Known for its excellence in statistics and related fields, ISI offers a range of programs from Bachelor's to Junior Research Fellowships. The admission test is scheduled for May 12, 2024. Eligibility varies by program, generally requiring a background in Mathematics and English for undergraduate courses and specific degrees for postgraduate and research positions. Application fees are ₹1500 for male general category applicants and ₹1000 for females. Applications are open to Indian and OCI candidates.
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Viral interaction with host cell sumoylation system
1. Viral Interaction with Host cell
SUMOylation system
R. SANTHAMANIR. SANTHAMANI
I. SOPHIAI. SOPHIA
Ph.D. StudentPh.D. Student
Division of VirologyDivision of Virology
Indian Veterinary Research InstituteIndian Veterinary Research Institute
MukteswarMukteswar
Uttarakhand.Uttarakhand.
2. Contents
1. What is sumoylation?
2. Discovery
3. Sumoylation pathway
4. Importance of sumoylation
5. Immunity and sumoylation
6. Viruses and sumoylation
7. What we gain?
05/08/14 Viruses and SUMOylation 2
4. DISCOVERY
Discovered independently
Study of Pro-Pro and Pro-NA interactions - Yeast 2-hybrid screens
(Boddy et al., 1996; Okura et al., 1996; Shen et al., 1996)
Biochemical analysis of nuclear transport component, RanGAP1
(Matunis et al., 1996; Mahajan et al., 1997)
cDNA mapping of human chromosome 21
(Lapenta et al., 1997)
known by
UBL1 (Shen et al., 1996)
Sentrin (Kamitani et al., 1997)
GMP1 (Matunis et al., 1996)
hSMT3C (Lapenta etal., 1997)
05/08/14 Viruses and SUMOylation
known to be proteins involved in
Sumoylation - SUMO proteins
4
5. Sumoylation pathway
Between lysine residue of
substrate and C- terminal GG motif
of SUMO
Consensus motif Ψ-K-x-D/E
Between lysine residue of
substrate and C- terminal GG motif
of SUMO
Consensus motif Ψ-K-x-D/E Sumoylat
ed
protein
(Desterro et al., 1997)05/08/14 Viruses and SUMOylation 5
6. Why Sumoylation system is
needed??
Sumolytion of vital cell
proteins pRB, PML and
RepA protein
Targeted transport
between nucleus and
cytoplasm
Gives stability to many
labile proteins – highly
folded structure
(Bayer et al., 1998)
05/08/14 Viruses and SUMOylation 6
8. Sumoylation of RIG 1, MDA 5 and Pellino 1
Upregulation of IFN production
Represses viral replication
Sumoylation of RIG 1, MDA 5 and Pellino 1
Upregulation of IFN production
Represses viral replication
05/08/14 Viruses and SUMOylation
Immunity and sumoylation …
(Zeng et al., 2010 & Wilson et al., 2012)
Innate immunity
8
9. 05/08/14 Viruses and SUMOylation
TLR PATHWAY
9
Immunity and sumoylation…
(Kim et al., 2011)
10. RLR PATHWAY
(Zeng et al., 2010)
Sumoylation of RIG 1 and MDA 5
05/08/14 Viruses and SUMOylation 10
Immunity and sumoylation…
Type
I IFN
11. Genetically encoded proteins - target the invading
viruses
Expressed at a constant level
Allows the viral infection to be halted quickly
Genetically encoded proteins - target the invading
viruses
Expressed at a constant level
Allows the viral infection to be halted quickly
05/08/14 Viruses and SUMOylation
Immunity and sumoylation …
Intrinsic immunity
11
(Everett et al., 2009)
12. Members of TRIM family of
proteins
Sumoylation of TRIM family proteins play
a role in antiviral activity
TRIM5α – retrovirus infections
TRIM5α has SIM motif to bind
with sumoylated CA of MLV
05/08/14 Viruses and SUMOylation
(Nakayama et al., 2012)
Intrinsic immunity
12
Immunity and sumoylation…
14. 05/08/14 Viruses and SUMOylation
Viruses and Sumoylation
Sumoylation process is exploited by viral pathogen to regulate their
activity
Many of the DNA viruses use sumoylation for targeting their vital
proteins to the nucleus to exploit host cell nuclear machinery
14
15. Virus Protein Function References
Adenovirus E1B-55K Transformation Endter et al., 2001
Adeno-associated virus Rep 78 Latency Weger et al., 2004
Epstein-Barr virus Rta (FRLF1)
EBNA3C
Lytic activation
Transcription
Chang et al., 2004
Rosendorff et al., 2004
Moloney murine
leukemia virus
CA Early stage of infection Yeuh et al., 2006
Human T cell leukemia
virus
Tax Induction of cancer Lamsoul et al., 2005
Papillomavirus E1
E2
Replication
Transcription of oncogenes
E6 , E7
Rangasamy et al., 2000
Marusic et al., 2010
Parainfluenza virus 5 P Replication Sun et al., 2011
05/08/14 Viruses and SUMOylation
Sumoylation of viral proteins
15
Viruses and sumoylation…
16. 05/08/14 Viruses and SUMOylation
Viruses have evolved to exploit further this intricate mechanism for
their own benefit
vProteins
Mimic sumoylation enzymes
Act as STUbLs
Targets sumoylation enzymes
Modulate sumoylation of specific host SUMO
substrates
Can viruses exploit more …? If so…Can viruses exploit more …? If so…
how???how???
16
(Chang et al., 2010)
Viruses and sumoylation…
17. 05/08/14
Viral interaction with host cell sumoylation
system
vProteins that mimic
sumoylation enzymes
KSHV – KbZIP
Binds with
SUMO
Sumoylate the binding
partners - p53 & pRB
SIM
motif
SIM
motif
SUMO
ligase
(Pennella et al., 2010)
Viruses and sumoylation…
Favourable for virus?
18. 05/08/14
Viral interaction with host cell sumoylation
system
vProteins that act as STUbLs
HSV – ICP0 protein
Bind to sumoylated PML
Ubiquitination
and
proteasomal
degradation
of
PML
Act as
Ubiquitin
ligase
SIM
like
motif
SIM
like
motif
(Perry et al., 2008)
Viruses and sumoylation…
19. 05/08/14
Viral interaction with host cell sumoylation
system
vProteins that targets
sumoylation enzymes
AdenovirusAdenovirus
Sumoylation
reduced
Eg. PML
(Boggio et al., 2004)
Viruses and sumoylation…
20. 05/08/14
Viral interaction with host cell sumoylation
system
HPV L2HPV E6
Viral cycle
(Heaton et al., 2011)
Sumo ligase
Sumoylating pRB
Maintains cell
in
quiescent
Ebola
virus
VP35
Sumoylation of
IRF7
Transcriptin of
IFN reduced
(Chang et al., 2009)
Viruses and sumoylation…
21. 05/08/14
Viral interaction with host cell sumoylation
system
vProteins that modulatevProteins that modulate
sumoylation of specific hostsumoylation of specific host
SUMO substratesSUMO substrates
Adenovirus E1A,
Papilloma virus E7
pRB
Maintains cell at definite stage of cell cycle
Cell enters
S-Phase
*favourable
for virus
replication
E2F
(Ledl et al., 2005)
Viruses and sumoylation…
22. 05/08/14
Viral interaction with host cell sumoylation
system
p53 - remains in nucleus
Cell cycle arrest, apoptotic signalling
in
viral infected cells
Adenovirus E1B
Sumoylates p53 &
targets it to cytoplasm,
makes it non-
functional
Contd…
Sumo
ligase
Sumo
ligase
(Lazo et al., 2011)
Viruses and sumoylation…
24. 05/08/14 Viruses and SUMOylation
What we gain??..
Better understanding of
Current knowledge on virus cell interaction
Nuclear targeting system
Signalling systems are regulated by sumoylation
Cellular regulatory functions
Some aspects of pathogenesis of Cancer
24
25. 05/08/14 Viruses and SUMOylation
OnlyOnly
knowledge??..knowledge??..
SUMO gene fusion technology for expressing labile proteins like
granzyme
If attaching SUMO to the N-terminus of poorly expressed proteins
dramatically enhances the level of expression
(Butt et al., 2005)
25
26. 05/08/14 Viruses and SUMOylation 26
Sumoylation is an essential PTM system in eukaryotes
Plays vital role in PTM of critical protein involved in overall cell signalling
systems including signalling pathways of intrinsic and innate immunity
Vital for transport of proteins between cytosol and nucleus
There are established intricate connections between sumoylation, viral
infection and cancer pathogenesis
SUMO fusion technology is a promising technique for bulk expression of
difficult to express proteins
May be having important role in prion pathogenesis but needs to be
investigated
To conclude…To conclude…
27. 05/08/14 Viruses and SUMOylation
Future….????Future….????
Role of Sumoylation in prion diseases?
For bulk production of recombinant antibodies ?
Targeted delivery to nucleus by sumoylation?
Drugs/chemicals/therapeutics with property of
controlled regulation of sumoylation for treating
cancer and viral infections?
27