Bidirectional Grammar and Bidirectional Optimization - CiteSeerX
Main Topics of the lecture Introduction. One-step growth ...DNA viruses replicate their genetic...
Transcript of Main Topics of the lecture Introduction. One-step growth ...DNA viruses replicate their genetic...
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Main Topics of the lecture
• Introduction.
• One-step growth curve.
• Steps of multiplication cycle.
• Attachment.
• Penetration (entry).
• Uncoating.
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Introduction
• Studies with the bacteriophages (at 1940/50s) and mammalian cell culture have revolutionized the progress of understanding virus replication.
• Every virus family employs a unique strategy for replication.
• One important concept to unify and simply the replication process was proposed by David Baltimore at 1978, to assign viruses to one of six classes based on their genome structure and the pathways they use to produce their mRNAs.
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I I II III IV V VI
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Steps of Virus Replication
• Attachment to target cell.
• Penetration (entry) from cell membrane.
• Uncoating.
• Expression (transcription and translation) of
viral proteins.
• Replication of the viral nucleic acid.
• Virus assembly
• Maturation and release.
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Virus Replication
Virus Entry and Uncoating
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Steps in Replication خطوات دورة تكاثر الفيروس
cycle of virus
Attachment األتصال I - Through receptors من خالل مستقبالت
CD4 HIV
Ig Poliovirus
Heparan sulfate HSV, Adenovirus
II - Random collision العشوائي التصادم
T- cell
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Attachment
• To initiate infection, the virus must be able to bind to target cell.
• Binding occurs between:
- Ligands on the virus surface (viral attachment proteins)
- Receptors on the plasma membrane of cell.
• Although there is a degree of specificity, quite different viruses may utilize the same receptor and, conversely, viruses in the same family or genus may use different receptors
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Virus attachment
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Examples:
• Influenza viruses: Viral Haemagglutinin (HA) peplomer
Sialic acid containing cell receptor
• HIV: Viral surface glycoprotein gp120 subunit SU binds to cellular CD4 receptor.
Then the complex binds to a second cell receptor ‘fusin’ which displaces SU and brings TM subunit into contact with cell membrane.
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Penetration (Entry)
• Following attachment, the virus enters the cell by one of two means:
1- Endocytosis; Receptor-mediated Endocytosis A- Fusion in Endosome ex: Influenzavirus B- Lysis of Endosome ex: Adenovirus
2- Fusion; Membrane fusion Ex: HIV
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Penetration (Entry)
• Following attachment, the virus enters the cell by one of two means:
1- Endocytosis:
• Receptor mediated endocytosis is a normal cell mechanism for
the uptake of macromolecules.
• Many enveloped and nonenveloped viruses use this essential cell
function to initiate infection.
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Steps of Endocytosis: 1- Virion attachment to receptors, which cluster at clathrin-coated
pits.
2- Endocytosis into clathrin-coated vesicles.
3- Vesicles enter the cytoplasm
4- After removal of the clathrin coat, vesicle fused with the endosome (acidic prelysosomal vacuoles).
5- Acidification within the vesicle triggers changes in virion proteins and surface structures.
6- These changes lead to the release of virus in the cytoplasm (e.g. fusion with the endonsomal membrane in influenza).
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Entry الدخول
Receptor-mediated Endocytosis التحوصل من خالل مستقبالت
Fusion in Endosome االندماج في األ ندوسوم Influenza virus
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Entry الدخول
Receptor-mediated Endocytosis التحوصل من خالل مستقبالت
Lysis of Endosome تحلل األ ندوسوم Adenovirus
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• F (fusion) glycoprotein present in some viruses causes the
envelope of these viruses to fuse directly with the plasma
membrane of the cell.
• This allows the nucleocapsid to be released directly into the
cytoplasm.
• e.g. Paramyxoviruses and some other enveloped viruses
2- Fusion:
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Entry الدخول
Membrane Fusion االندماج الغشائي
Paramyxovirus + HIV
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Aim: To expose viral genes for transcription and replication
1- Complete uncoating:
• Occurs in enveloped viruses that enter the cell by fusion with plasma or endosomal membrane.
• The nucleocapsid is discharged directly into the cytoplasm and transcription occurs directly.
2- Partial uncoating: • Occurs with some naked viruses.
• Only certain capsid proteins are removed and the viral genome expresses all its functions without ever being released from the virion core.
3- Uncoating
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Uncoating التـقـشـر 3. - Direct or Partial uncoating
مباشر أو جزئي Paramyxovirus + HIV
Endosome …. Conformational changes
تغيرات شكلية Influenza + Adenovirus
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التكاثر وإنتاج بروتينات الفيروس 4.
Replication and viral protein production
o Replication: Copy (RNA or DNA); duplication.
o Synthesis: Translation of mRNA into Viral proteins.
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Baltimore Classification
All viruses must generate positive strand mRNAs from their genomes,
in order to produce proteins and replicate themselves.
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DNA Viruses
DNA viruses Replicate in the Nucleus Except: Poxvirus
Most DNA viruses encode DNA polymerase
(Except small DNA viruses; parvoviruses and papillomaviruses)
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DNA viruses replicate their genetic material by:
Bidirectional replication from a circular substrate The process include:
“theta-form” intermediate (eg, papillomaviruses),
“rolling circle” mechanism
Replication from a linear substrate Examples include adenoviruses
Replication via an RNA intermediate Hepadnaviruses (hepatitis B virus) are unique since they contain a
partially dsDNA genome that must be converted into an RNA form
by the viral reverse transcriptase (RT) during the virus life cycle .
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DNA REPLICATION
DNA
5’
3
’
NICKED
DNA
5’
3
’ 5’
3’
5’
3’ 5’ 3’
SIMPLIFIED SCHEME
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Baltimore Classification
All viruses must generate positive strand mRNAs from their genomes,
in order to produce proteins and replicate themselves.
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I- Double stranded DNA
A- Nucleus ex: Adenovirus and Herpesvirus
B- Cytoplasm ex: Poxvirus
+ -
Replication Transcription
mRNA
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Nucleus ex: Parvovirus
II- Single stranded DNA
Template D.STD. intermediate
Replication
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Baltimore Classification
All viruses must generate positive strand mRNAs from their genomes,
in order to produce proteins and replicate themselves.
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RNA Viruses
All RNA viruses Replicate in the Cytoplasm Except: Orthomyxoviruses (influenza A & B)
Borna disease virus,
Hepatitis delta virus
Retrovirses
All RNA viruses encode RNA dependent RNA polymerase
Except; Retrovirus
RNA Genome:
1- Copy RNA
2- Translate mRNA
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RNA Genome (-) and (-,+);
The virus carry the Enzyme
Noninfectious
RNA Genome (+);
The virus produces the Enzyme
Infectious
Enzyme: RNA dependent RNA polymerase
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III- Double stranded RNA
Cytoplasm ex: Reovirus
Segmented
Replication
Template monocistronic mRNA
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DOUBLE-STRANDED RNA GENOMES
AAA (+ve) sense mRNA
Double-stranded genomic RNA If used, RNA modifying enzymes are packaged in virion.
RNA polymerase must be packaged in virion.
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IV- Single stranded RNA (+) Sense
Replication
Template -
+
+
RNA
RNA
RNA
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PLUS (POSITIVE) SENSE RNA GENOMES
AAA (+ve) sense mRNA
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V- Single stranded RNA (-) Sense
Cytoplasm ex: Paramyxovirus
Non-Segmented
Replication
Transcription
+
-
-
RNA
RNA
RNA
Template monocistronic mRNA
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MINUS (NEGATIVE) SENSE RNA GENOMES
AAA (+ve) sense mRNA
(-ve) sense genomic RNA
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V- Single stranded RNA (-) Sense
• Nucleus ex: Orthmyxovirus
• Segmented
Replication
Transcription
+
-
-
RNA
RNA
RNA
Template monocistronic mRNA
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MINUS (NEGATIVE) SENSE RNA GENOMES RNA polymerase must be packaged in virion.
AAA (+ve) sense mRNA
(-ve) sense genomic RNA
If used, RNA modifying enzymes are packaged in virion.
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VI- Single stranded RNA (+) Sense With DNA Intermediate
Retrovirus
Template D.STD. DNA intermediate
+ RNA
Cytoplasm
Nucleus
RT
+ RNA
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RETROVIRUSES
DS
DNA
+VE
RNA
DS
DNA
Reverse transcriptase must be packaged in virion.
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VII- Double stranded DNA With RNA Intermediate
Hepadnavirus
Template S.STD. RNA intermediate
DNA
Cytoplasm
Nucleus
RT
DNA
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One-step Growth Curve
• Defined by classical studies on cell culture, in which multiple
cultures are infected simultaneously.
• The increase in infectious virus over time is followed by
sequential sampling and titration.
Cell-free and Cell-associated
• Shortly after infection, the inoculated ‘Cell-free’ virus
disappears (extra- and intra-cellular).
• This period extends for 2-12 hours, until first progeny viruses
become detectable (Eclipse Period)
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One-step Growth Curve
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One - Step Growth Cycle:
Eclipse period (11H) Post-infection (PI) Genome Free inside cell No infectious Particles
Synthetic phase
(12 H) (PI) Infections particles
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Typical Growth Curve:
10
8
6
4
2
PFU/ml
Hours post adsorption
4 12 20 28 36 44 50
Total or intracellular + extracellular
Extracellular
Eclipse period
Latent period
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One - Step Growth Cycle:
Eclipse period
Synthetic phase
Latent period (18 H) P.I.
No extracellular virus
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Assembly + Release التجمع والتحرر 5.
األحماض النووية - البروتينات التركيبية - األنزيمات الفيروسية -
موقع التجمع يعتمد على موقع التكاثر -
Picornavirus , Poxvirus , Reovirus…etc
Cytoplasm
Adenovirus , Polyomavirus …etc
Nucleus
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Virus Assembly
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Assembly + Releaseالتجمع والتحرر 5.
Maturation النضج - - Infectious
- Conformational changes
Fo F1 + F2 paramyxovirus
Fusion protein
Cleavage Proteases
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Release التحرر
- I التحلل Lysis
Non - enveloped
Lytic viruses
- II التبرعم Budding
Enveloped
I + II death of cell (CPE)
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Vaccines and antiviral drugs
Active immunizationالتحصين النشط -
Vaccinesاللقاحات -
Agانتجينات الفيروس -
الجلد ، داخل الجلد ، األنف ، العضل ، الوريد، الفم -
Agحث جهاز المناعة ألنتاج أجسام مضادة ضد -
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نوعية متخصصة / Antibodiesأجسام مضادة
Immunoglobulins (Ig)
(Adaptive) Acquired immunity
Live Vaccine
Killed Vaccine
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ال يسبب مرضًا. 1
-Live attenuated Vaccine
استحثاث مقامه طويل إلمد مكتسبة.2
Pox – Yello – Polio – Measles
يجب أن يكون مامونًا. 3
يجب أن يكون ثابتًا. 4
شروط فعالية اللقاحات
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Natural Passive immunityالمناعة السالبة الطبيعية
Maternal immunityمناعة األم المنقولة عبر المشيمة
Passive immunizationالتحصين السالب
المناعة السالبة الصناعية
(HBIG) - HBV
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Antiviral drugsالمضادات الفيروسية
Acyclovirاسايكلوفير
Herpesviruse
Viral DNA synthesis
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Amantadine / Rimantadine
Influenza virus
Type-A
Pentration
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Ribavirin
RSV
HCV
(Guanine)
RNA synthesis
Zidovudine (AZT)زيدوفيودين
(HIV)