PCR (Polymerase Chain Reaction)

PCR

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics.

The majority of PCR methods rely on thermal cycling. Thermal cycling exposes reactants to repeated cycles of heating and cooling to permit different temperature-dependent reactions – specifically, DNA melting and enzyme-driven DNA replication. PCR employs two main reagents – primers (which are short single strand DNA fragments known as oligonucleotides that are a complementary sequence to the target DNA region) and a DNA polymerase. In the first step of PCR, the two strands of the DNA double helix are physically separated at a high temperature in a process called Nucleic acid denaturation. In the second step, the temperature is lowered and the primers bind to the complementary sequences of DNA. The two DNA strands then become templates for DNA polymerase to enzymatically assemble a new DNA strand from free nucleotides, the building blocks of DNA. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the original DNA template is exponentially amplified.

Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the thermophilic bacterium Thermus aquaticus. If the polymerase used was heat-susceptible, it would denature under the high temperatures of the denaturation step. Before the use of Taq polymerase, DNA polymerase had to be manually added every cycle, which was a tedious and costly process.

Applications of the technique include DNA cloning for sequencing, gene cloning and manipulation, gene mutagenesis; construction of DNA-based phylogenies, or functional analysis of genes; diagnosis and monitoring of hereditary diseases; amplification of ancient DNA; analysis of genetic fingerprints for DNA profiling (for example, in forensic science and parentage testing); and detection of pathogens in nucleic acid tests for the diagnosis of infectious diseases.

CRISPRCas9

CRISPRCas9

CRISPR-Cas9 is a method of genome editing that exploits a natural DNA-snipping enzyme in bacteria, called Cas9 (CRISPR-associated protein 9) to target and edit particular genes. CRISPR stands for Clustered regularly interspaced short palindromic repeats, which are segments of DNA of a particular structure found widely in bacteria and archaea (prokaryotes). In the wild, the CRISPR-Cas9 system is part of the prokaryotic immune system, which can snip out of the genome DNA acquired from foreign sources such as phages (bacterial viruses). The same molecular machinery is now being used to enable genetic material to be cut from and pasted into the genomes of other organisms, including eukaryotes such as humans. It might offer a tool for curing genetically based diseases.

DNA has become a versatile polymeric substrate for making nanotechnological structures and artificial molecular-scale machinery for computation, pattern formation, and nanoscale assembly. For several decades now, these efforts have drawn on methods developed in and for biotechnology, and similarly they are likely to find ways of exploiting the advantages of the new technique called CRISPR/Cas9 for manipulating DNA. #CRISPRCas9

CRISPR-Cas9 is a method of genome editing that exploits a natural DNA-snipping enzyme in bacteria, called Cas9 (CRISPR-associated protein 9) to target and edit particular genes. CRISPR stands for Clustered regularly interspaced short palindromic repeats, which are segments of DNA of a particular structure found widely in bacteria and archaea (prokaryotes). In the wild, the CRISPR-Cas9 system is part of the prokaryotic immune system, which can snip out of the genome DNA acquired from foreign sources such as phages (bacterial viruses). The same molecular machinery is now being used to enable genetic material to be cut from and pasted into the genomes of other organisms, including eukaryotes such as humans. It might offer a tool for curing genetically based diseases.

DNA has become a versatile polymeric substrate for making nanotechnological structures and artificial molecular-scale machinery for computation, pattern formation, and nanoscale assembly. For several decades now, these efforts have drawn on methods developed in and for biotechnology, and similarly they are likely to find ways of exploiting the advantages of the new technique called CRISPR/Cas9 for manipulating DNA.

Antibody (Immunoglobulin)

Antibody:
Antibody also called immunoglobulin, a protective protein produced by the immune system in response to the presence of a foreign substance, called an antigen.
When an alien substance enters the body, the immune system is able to recognize it as foreign because molecules on the surface of the antigen differ from those found in the body.
Antibodies are produced by specialized white blood cells called B lymphocytes (or B cells). When an antigen binds to the B-cell surface, it stimulates the B cell to divide and mature into a group of identical cells called a clone. The mature B cells, called plasma cells, secrete millions of antibodies into the bloodstream and lymphatic system.

Antibody structure:
The four-chain structure of an antibody, or immunoglobulin, molecule. The basic unit is composed of two identical light (L) chains and two identical heavy (H) chains, which are held together by disulfide bonds to form a flexible Y shape. Each chain is composed of a variable (V) region and a constant (C) region.

Antibodies are grouped into five classes according to their constant region.
Each class is designated by a letter attached to an abbreviation of the word immunoglobulin: IgG, IgM, IgA, IgD, and IgE.

CORONAVIRUS

Coronaviruses (CoV) are a large family of viruses that cause illness ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS-CoV) and Severe Acure Respiratory Syndrome (SARS-CoV). A novel coronavirus (nCoV) is a new strain that has not been proviously identified in humans.

Coronaviruses are a family of viruses that cause disease in animals. Detailed investigations found that SARS-CoV was transmitted from civet cats to human and MERS-CoV from dromedary camels to humans. Several known coronaviruses are circulating in animals that have not yet infected humans.

The new coronavirus, officially called Covid-19 currently has fatality rate between 0.7 per cent to 3.4 per cent. This is much lower than fatality rates for Mers (30 per cent) and SARS (10 per cent), but still a significant threat. However, the new coronavirus (Covid-19) is spreading fast. The bulk cases and fatalities have been confined to China, but the virus is spreading internationally.

The source of the coronavirus is believed to be a "wet market" in Wuhan which sell both dead and live animals including fish and birds. Such markets pose a heightened risk of viruses, jumping from animals to humans because hygiene standards are difficult to maintain if live animals are being kept and butchered on site. Typically, they are also densely packed.

The animal source of the latest outbreak has not yet been identified, but the original host is thought to be bats. Bats were not sold at the Wuhan market but may have infected live chickens or other animals sold there.

Bats are host to a wide range of zoonotic viruses including Ebola, HIV and rabies.

Scientist in China believe that Covid-19 has mutated into two strains, one more aggressive than the other, which could make developing a vaccine more complicated.

It is impossible to say which way the disease will go but, on its current trajectory, it is likely to spread to more countries, affecting many more people. The number of cases is beginning to decrease in China but is increasing in the rest of the world.

Initial common symptoms of Covid-19 include fever, dry cough, tiredness and a general feeling of being unwell. In more severe cases, infection can cause pneumonia, severe acute respiratory syndrome, kidney failure and even death. Symptoms are thought to appear between 2 and 10 days later after contracting the virus, but it may be up to 24 days

The virus is spread via droplets when a person coughs or sneezes. The droplets land on surfaces and are picked up on the hands of others and spread further. People catch the virus when they tough their infected hands to their mouth, nose or eyes. Standard recommendations to prevent infection include regular hand washing, covering mouth and nose when coughing and sneezing, thoroughly cooking meat and eggs. Avoid close contact with anyone showing symptoms or respiratory illness such as coughing and sneezing.

Various crazy conspiracy theories have been circulating that the virus somehow escaped from a Chinese lab, either by accident or design. However, that is categorically untrue and scientists studying its genetic code have linked it to bats. It probably then jumped to another animal, which passed it on to humans.

The 1918 Spanish Influenza or the H1N1 virus remains the most devastating flu pandemic in the modern history. The disease swept around the globe and is estimated to have caused between 50 to 100 million deaths. A version of the same virus was also behind the 2009 swine flu outbreak, thought to have killed as many as 575,400 people.

Other major influenza outbreaks include Asian flu in 1957, which led to roughly 2 million deaths, and Hong Kong flu which killed 1 million people 11 years later.

But coronavirus outbreaks have so far been far smaller. Sars eventually spread to 27 countries in total, infecting around 8000 people and killing 700

Dengue Fever

Dengue fever is a painful, debilitating mosquito borne disease caused by any one of four closely related dengue viruses. These viruses are related to the viruses that cause West Nile infection and yellow fever.

An estimated 400 million dengue infections occur worldwide each year, with about 96 million resulting in illness. Most cases occur in tropical areas of the world, with the greatest risk occurring in the Indian sub continent, Southeast Asia, Southern China, Taiwan, the Pacific Islands, the Caribbean (except Cuba and the Cayman Islands), Mexico, Africa, Central and South America (except Chile, Paraguay, Argentina)

Dengue fever is transmitted by the bite of an Aedes mosquito infected with a dengue virus. Its peak biting periods are early morning and before dusk. The mosquito becomes infected when it bites a person with dengue virus in their blood. It cant spread directly from one person to another person.

Transmission of Dengue virus

Symptoms of Dengue fever usually begin four to six days after infection and last for up to 10 days, and may include sudden high fever, severe headaches, pain behind the eyes, severe joint and muscle pain, fatigue, nausea, vomiting, skin rash which appear two to five days after the onset of fever,mild bleeding such as nose bleeding, bleeding gums or easy bruising.

Sometimes symptoms are mild and can be mistaken for those of flu or another viral infection. Younger children and person who have never had the infection before tend to have have milder cases than older children and adults. However, serious problems can develop. These include dengue hemorrhagic fever, a rare complication characterized by high fever, damage of lymph and blood vessels, bleeding from the nose and gums, enlargement of the liver, and failure of the circulatory system. The symptoms may progress to massive bleeding, shock and death. This is called dengue shock syndrome (DSS).

People with weakened immune systems as well as those with a second or subsequent dengue infection are believed to be at greater risk for developing dengue hemorrhagic fever.

Doctors can diagnose dengue infection with a blood test to check for the virus or antibodies to it.

There is no specific medicine to treat dengue infection, If you think you may have dengue fever, you should use pain relievers with acetaminophen and avoid medicines with aspirin, which could worsen bleeding, You should also rest, drink plenty of fluids and see your doctor. If you start to feel worse in the first 24 hours after your fever goes down, you should get to a hospital immediately to be checked for complications.

The best way to prevent the disease is to prevent bites by infected mosquitoes, particularly if you are living in or travelling to a tropical area. This involves protecting yourself and making efforts to keepk the mosquito population down.

To protect yourself
Use mosquito repellents, even indoors
When outdoors, wear long sleeved shirts and long pants tucked into socks
When indoors, use air conditioning if available
Make sure window and door screens are secure and free of holes. If sleeping areas are not screened or air conditioned, use mosquito nets
If you have symptoms of dengue, speak to your doctor

To reduce the mosquito population, destroy the mosquito breeding grounds and spray insecticide in the affected areas. These include old tires, cans. or flower pots that collect rain. Regularly change the water in outdoor bird baths and pet's water dishes.

If someone in your home gets dengue fever, be especially vigilant about efforts to protect yourself and other family members from mosquitoes. Mosquitoes that bite the infected family member could spread the infection to others in your home.

FASTER WAY TO PRODUCE SPECIFIC HUMAN ANTIBODIES USING NANOPARTICLES

Treating patient derived B cells with nanoparticles coated with CpG oligonucleotides to stimulate plasma cell production and challenge antigens to designate what kind of antibody the B cells should produce has resulted in the generation of specific, high affinity antibodies in just a few days that can recognize several strains of a pathogen at the same time. The researchers have already produced antibodies to a variety of bacterial and viral antigens, including tetanus toxoid and several strains of influenza, and were able to generate anti HIV antibodies from B cells donated by healthy volunteers who did not have the disease.

The new technique also eliminates the need for previous exposure to the pathogens, either by vaccination or infection.

"Our technique should allow the production of these antibodies within a shorter time frame in vitro and without the need for vaccination or blood/serum donation from recently infected or vaccinated individuals," said Dr. Facundo Batista, who led the team from the Francis Crick Institute in London, the Ragon Institute of Massachusetts General Hospital, MIT and Harvard. "In addition, our method offers the potential to accelerate the development of new vaccines by allowing the efficient evaluation of candidate target antigens."

Antibodies are produced by white blood cells called B cells, which recognize the calling card of a bacteria or virus called an antigen, and transform into plasma cells tailored to produce large numbers of antibodies to that specific antigen that fight off the disease. That's what happens in the body. When scientists tried to reproduce the process in the lab, they ran into problems getting the B cells to make the specific kind of plasma cells they needed because the challenge antigens were missing.

It was easy to get the B cells to proliferate by adding short DNA fragments called CpG oligonucleotides into their culture medium. CpG oligonucleotides activate a protein inside B cells TLR9, but TLR9 enthusiastically stimulates every B cell in the sample to respond, not just the tiny fraction capable of producing a particular antibody. Batista and his colleagues attached both CpG oligonucleotides and real challenge antigens to nanoparticles, added them to B cell cultures, and the plasma cells that resulted were both abundant and pathogen specific.

The team hopes their approach will help researchers produce therapeutic antibodies to treat infectious disease and other conditions, such as cancer.

For more information, go to the Journal of Experimental Medicine
http://jem.rupress.org/cgi/doi/10.1084/jem.20170633?PR
https://www.eurekalert.org/pub_releases/2017-07/rup-rdn071717.php

BACTERIOPHAGES: SMALL THINGS CONSIDERED

Bacteriophages ("phages", for short) are viruses that infect prokaryotes (bacteria and archaea), harnessing the resources of the host cell to replicate vast numbers of themselves, eventually causing the cell to lyse and release the phage progeny, which then find new hosts and repeat the cycle. But that's just the textbook definition. What really hooks us in that some phages look just like lunar landers sent from alien spaceships. Merry Youle, one of STC's very own, has written a charming paean to her beloved subjects, a full length book all about "what makes the phages so fascinating, so intriguing, and so important."

Youle tells us, "This book was born of love, exasperation, and wonderment." Youle holds that phages are deserving of far more ink, and respect, than they've thus far received. They exist everywhere where their hosts thrive, including hydrothermal vents, acidic springs, the arctic tundra, and your own gut. They impact geothermal cycles, algal booms, and biodiversity. They are useful tools for genetic manipulation in the lab as well as in nature. and can serve as allies in treating bacterial infections.

Enterobacteriophage T4

http://schaechter.asmblog.org/schaechter/2017/07/a-star-studded-phantastic-voyage-of-phages.html

These "Indestructible" Animals Would Survive a Planet-Wide Apocalypse

Even the most catastrophic astrophysical events couldn't wipe out the hardy tardigrade, researchers report.

A magnified view of a tardigrade, also known as a water bear

The world's most robust animals may very well survive until the sun stops shining.

Also known as water bears, tardigrades are tiny water dwelling creatures famed for their resiliency. The eight legged invertebrates can survive for up to 30 years without food or water and can endure wild temperature extremes, radiation exposure, and even the vacuum of space.

"Tardigrades are extremely hardy animals," says Thomas Boothby, a tardigrade researcher at the University of North Carolina. "Scientists are still trying to work out how they survive these extremes."

At a minimum, all of Earth's oceans would have to boil away to completely wipe out all life on the planet. Although Boothby said tardigrades are only known to survive high temperatures when dry and those species living in the sea would likely die before the waters boiled , tardigrades are still expected to avoid extinction until our sun swells up and becomes a red giant roughly six billion years from now, according to researchers who investigated the effects of various doomsday scenarios.


For details Tardigrades: The Indestructible Animals

Discoverer of penicillin Alexander Fleming warned against its overuse and the risk of resistant microorganisms as early as 1945, in his Nobel Prize lecture

"The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant.

Here is a hypothetical illustration. Mr. X has a sore throat. He buys some penicillin and gives himself, not enough to kill the streptococci but enough to educate them to resist penicillin. He then infects his wife. Mrs. X gets pneumonia and is treated with penicillin. As the streptococci are now resistant to penicillin the treatment fails. Mrs. X dies. Who is primarily responsible for Mrs. X's death? Why Mr. X whose negligent use of penicillin changed the nature of the microbe.

Moral: If you use penicillin, use enough"

Sir Alexander Fleming shared the Nobel Prize in Physiology or Medicine in 1945 with Howard Florey and Ernst Boris Chain for his discovery of the world's first antibiotic substance benzylpenicillin (Penicillin G) from the mould Penicillium notatum in 1928. He also discovered the enzyme lysozyme in 1923.

Fleming's Nobel Lecture reached from here:Nobel Lecture by Sir Alexander Fleming on December 11, 1945

Yoshinori Ohsumi: Autophagy from begining to end

Yoshinori Ohsumi was influenced by his father, who was a professor of engineering at Kyushu University, He was familiar with academic life while he was growing up. But whereas his father worked in a very industrially oriented field, he was more interested in the natural sciences. In high school, he was interested in chemistry, so he entered the University of Tokyo to learn chemistry. He quickly discovered chemistry wasn't so attractive to him, because the field was already quite established. But he was lucky, he thinks, because the early 1960's was the golden age of molecular biology. He decided he wanted to work on that instead.

There were not very many molecular biology labs in Japan at that time. He joined Dr. Kazutomo Imahori's lab as a graduate student to study protein synthesis in E. coli. Unfortunately, he did not get very good results in his work, and, when he had finished his graduate studies, he discovered it was very difficult to find a good position in Japan. So, on Dr. Imahori's advice, he took a postdoctoral position with Dr. Gerald Edelman at The Rockefeller University in New York.

As a graduate student, he had worked on E. coli., but in Dr. Edelman's lab he switched to working on mammalian cell and developmental biology. He was supposed to establish a system for in vitro fertilization in mice,  but he did not know very much about early embryology and he had only a very small number of eggs to work with. He grew very frustrated. Then, one and a half years later, Mike Jazwinski joined Edelman's lab, and he decided to work with him instead on studying DNA duplication in yeast. That was another huge leap for him, but it was also his first introduction to yeast cells, which he has worked with ever since.

Finally, he was offered a position as a junior professor in Yasuhiro Anraku's lab at the University of Tokyo and was able to return to Japan

For complete interview, read this 2012 interview conducted by Journal of Cell Biology, where Yoshinori Ohsumi explains his progress within the field of autophagy.

Autophagy genes are discovered by Yoshinori Ohsumi for the greatest benefit to mankind

Autophagy has been known for over 50 years but its fundamental importance in physiology and medicine was only recognized after Yoshinori Ohsumi's paradigm-shifting research in the 1990's.

The experiment by 2016 Medicine Laureate Yoshinori Ohsumi demonstrated that autophagy exists in yeast. Ohsumi studied thousands of yeast mutants and identified 15 genes that are essential for autophagy. But even more importantly, he now had a method to identify and characterize key genes involved in this process. This was a major break through and Ohsumi published the results in 1992. First key publication: Takeshige, K., Baba, M., Tsuboi, S., Noda, T, and Ohsumi, Y. (1992). Autophagy in yeast demonstrated with proteinase-defifient mutants and conditoins for its induction. Journal of Cell Biology 119, 301-3011

The term "autophagy" was coined by Christian de Duve in 1963. Our bodies are made up of cells that contain organelles, components with various functions, Albert Claude's research with the newly developed electron microscope and his methods for separating the various parts of pulverized cells using a centrifuge opened up new opportunities for studying cells in detail. In 1995, Christian de Duve discovered previously unknown organelles in the cell, lysosomes. These have important functions in decomposing different types of materials, such as bacteria and parts of cells that have worn out. In 1974 de Duve shared the Nobel Prize in Medicine for discovering the lysosome.

Thanks to Ohsumi and others following in his footsteps, we now know that autophagy controls important physiological functions where cellular components need to be degraded and recycled. Autophagy can rapidly provide fuel for energy and building blocks for renewal of cellular components, and is therefore essential for the cellular response to starvation and other types of stress. After infection, autophagy can eliminate invading intracellular bacteria and viruses. Autophagy contributes to embryo development and cell differentiation. Cells also use autophagy to eliminate damaged proteins and organelles, a quality control mechanism that is critical for counteracting the negative consequences of aging.

Disrupted autophagy has been linked to Parkinson's disease, type 2 diabetes and other disorders that appear in the elderly. Mutations in autophagy genes can cause genetic disease. Disturbances in the autophagic machinery have also been linked to cancer. Intense research is now ongoing to develop drugs that can target autophagy in various diseases.

Nobel Prize 2016 in Physiology or Medicine

The 2016 Nobel Prize in Physiology or Medicine is awarded to Yoshinori Ohsumi for his discoveries of mechanisms for autophagy which was announced on 3rd October 2016

This year's Nobel Laureate discovered and elucidated mechanisms underlying autophagy, a fundamental process for degrading and recycling cellular components.

The word autophagy originates from the Greek words auto- meaning self and phagein- meaning to eat. Thus, autophagy denotes "self eating." Its a process whereby the eukaryotic cell can recycle part of its own content. This concept emerged during the 1960's, when researchers first observed that the cell could destroy its own contents by enclosing it in membranes, forming sack like vesicles that were transported to a recycling compartment, called lysosome, for degradation. Unlike other cellular degradation machineries, autophagy removes long lived proteins, large macro molecular complexes and organelles that have become obsolete or damaged. Difficulties in studying the phenomenon meant that little was known until, in a series of brilliant experiments in the early 1990's. Yoshinori Ohsumi used baker's yeast to identify genes essential for autophagy. He then went on to elucidate the underlying mechanisms for autophagy in yeast and showed that similar sophisticated machinery is used in our cells.

Ohsumi's discoveries led to a new paradigm in our understanding of how the cell recycles its content. His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection. Mutations in autophagy genes can cause disease, and the autophagic process is involved in several conditions including cancer and neurological disease.

Yoshinori Ohsumi is a professor at the Tokyo Institute of Technology since 2009 

Bacteria*Bioengineering*Storage

A new method of data storage that converts information into DNA sequences allows you to store the contents of an entire computer hard-drive on a gram's worth of E coli and perhaps considerably more than that.

Source:

Collection of Title of Dissertation (Updated)

       A Comprehensive Collection of Title of Dissertations Submitted by Students of M.Sc. Microbiology to The Central Department of Microbiology, Tribhuvan University

Find here more Collection of Title of Dissertation (from 1 to 172)  

173. Lower respiratory tract infection a socio-medical aspect. By: Punita Gauchan 

174. Study on performance of waste water  treatment plant at guheshwari. By: Chandra Shekhar Rajaure  

175. A prospective study on microbiology of lower respiratory tract infection and antibiotic sensitivity profile with interest in multidrug resistance and extended spectrum of betalactamase strains. By: Jaya Sharma   

176. Prevalence of Lymphatic filariasis in Parsa District of Nepal. By: Surath Upadhaya 

177. Field evaluation of the OPTimal test for the rapid diagnosis of malaria. By: Puspa Raj Pandey  

178. An epidemiological study of malaria in Kanchanur District during 2003. By: Deepak Joshi 

179. Microbiology of Bacteraemia and septicaemia in patients visiting Tribhuvan University, Teaching Hospital (TUTH) Kathmandu. By: Yadav Wagley 

180. Study on heavy metal resistant bacteria in the waste water treatment plant at Guheshwori. By: Anjita Rajbanshi 

181. Prevalence of catheter associated urinary tract infection as Hospital acquired infection in TUTH. By: Abhilasha Gurung 

182. Comparative evaluation of four different tests in the diagnosis of Visceral leishmaniasis in Nepal. By: Amin Khadka 

183. Microbial quality evaluation of milk and butter with special reference to the milk pathogens and MBRT test. By: Toya Nath Sapkota 

184. An epidemiological study of anti-tuberculosis drug resistance pattern in the pulmonary tuberculosis patients visiting national tuberculosis centre. By: Komal Raj Rijal 

185. A Hospital study of urinary tract infection among pregnant women visiting Lumbini Zonal Hospital, Butwal. By: Munal Subedi 

186. Study on the impairment of liver kindney and pancreas in Hepatitis B and C positive cases. By: Amrit M S Maharjan 

187. Enteropathogens associated with acute diarrhoea in patients visiting National Public Laboratory, Teku. By: Ranjan K. C 

188. Study on nasopharyngeal pneumococcal carriage enteroparasitic infectations in children. By: Bijaya Malla 

189. Study on the prevalence of Salmonella species from blood sample of the patients visiting national public health  laboratory, Teku. By: Sabina Shrestha 

190. Prevalence of Methicillin resistant Staphylococcus aureus (MRSA) in children visiting Kanti children's Hospitals. By: Santosh Thapa 

191. Bacteriological profile of bacteraemia and speticaemia among patients of infective endocarditis. By: Narayan Prasad Kandel 

192. Microbial study of chronic obstructive pulmonary disease in patients admitted in Nepal Medical College Teaching Hospital, Jorpati. By: Deepu Pudasaini

193A prospective study of urinary tract infections in female patients attending Kathmandu Model Hospital. By: Puja Shrestha 

194. Prevalence of Aeromonas in different clinical samples and water with special interest in Gastroenteritis. By: Nirajan Thapa Kshetry 

195. Serostatus of rheumatoid factor, c-reactive protein, antistreptolysin-o and uric acid in patients visiting OM Hospital and research centre. By: Raj Kumar Karki 

196.  Study of urinary tract infection among kidney transplant patients visiting National Public Health Laboratory, Teku.By: Gokarna Raj Ghimire 

197. Prevalence of vulvovaginal giardiasis in females attending gynecological outpatient department of Tribhuvan University Teaching Hospital. By: Bijaya Bajracharya 

198. Seroprevalence of torch in Nepalese women of childbearing age and evaluation of biochemical parameters. By: Pradeep Kafle 

199. Detection of enteric pathogens (Vibrio Cholerae and Escherichia coli 0157) in childhood diarrhoeal cases. By: Roshani Maharjan 

200. Prevalence of Urinary tract infection and candiasis of   pregnant women at community based reproductive health care & counseling center of Kirtipur Municipality. By: Sulochana Basnet (Mahat) 

201.  Detection of Enteropathogens (Salmonella spp, Shigella spp and Parasites) in the stool specimen of children suffering from diarrhea and admitted at kanti children Hospital. By: Diksha Khadka 

202. Evaluation of antimicrobial activities of some medical plants. By: D Radha 

203. Seroprev valence of hepatitis B and HIV among volunteer blood donors of Kathmandu. By: Dinesh Thapa 

204. Prevalence of lower respiratory tract pathogens (bacterial) in Nepalese HIV/AIDS Patients. By: Dipendra Gautam 

205. Study of Bacteraemia in malnourished children admitted to Kanti children's hospital. By: Prakash Chandra Amatya 

206. Recovery of sliver from used X-Ray films using alkaline protease extracted from Bacillus spp. By: Dal Bahadur Khatri 

207. Screening of soil bacillus species for ß lactamase activity. By: Niraj Nakarmi 

208. Genetic variability of Mycobacterium leprae in Nepal. By: Susan Pandey 

209. Prevalence of multidrug resistant strains with reference to extended spectrum beta-lactamase producing strains among the bacterial pathogens isolated from different clinical samples at Tribhuvan University Teaching Hospital. By:Rajdeep Bomjan 

210. Antibiotic susceptibility profile of bacterial pathogens in urinary trace infection with special reference to extended spectrum beta lactamase (ESBL) oridycubt straubs. By: Trishna Manandhar 

211. Study on Microbiology of urinary tract infection and the prevalence of multidrug resistant strains among the bacterial pathogens. By:Deepa Shrestha 

212. Tuberculosis and HIV co-infection in HIV-AIDS persons of Nepal. By: Govinda Prasad Dhungana 

213. Cross-sectional study of respiratory pathogenes and their antibiotic susceptibiligy pattern in Tribhuvan Unversity Teaching Hospital. By: Uma Shrestha 

214. Loop-mediated isothermal amplification for direct detection of mycobacterium tuberculosis in sputum samples. By: Ajaya Poudel 

215. A study on etiological agents of bacteraemia and antibiotic susceptibiligy pattern of isolates. By: Niroj Man Amatya 

216. Biodiversity and bioactivity of endophytic fungi of tsuga dumosa D. Don. By: Anjana Upadhaya 

217. Vermicomposting, enrichment of vermicompost by azotobacter chroococcum and response on phaseolus bean. By: Yukti Basnet 

218. Prevalence of malaria and hepatitis B among Nepalese blood donors. By: Bishnu Bhakta Dhungel 

219. Evaluation of different staining techniques (Ziehl neelsen stain, Kinyoun stain, Modified cold stain and fluorochrome stain) for the diagnosis of pulmonary tuberculosis. By: Deepika Shrestha 

220. Study of delta encotoxin immunocrossreactivity of bacillus thuringiensis isolates from khumbu base camp of the Everest Region. By: Upendra Thapa Shrestha 

221. Study of genetic polymorphism among bacillus thuringensis isolates from Khumbu Base Camp of Everest Region by randomly amplified polymorphic DNA polymerase Chain Reaction. By: Gyan Sundar Sahukhal 

222. Study of prevalence of enteric fever and the assessment of widal test in the diagnosis of typhoid fever. By: Samira Khatiwada 

223. A prospective study on etiology of diarrhea with reference to multiple drug resistant enteric bacterial pathogens. By: Sirjana Devi Shrestha 

224. Prevalence of intestinal parasitosis among HIV/HIDS patients of Kathmandu Valley and Dhulikhel. By: Sunil Maharjan 

225. Microbiological study among diarrhoeal children in relation to cyclospora and rotavirus infection. By: Chamala Lama 

226. Study of prevalence of intestinal parasitic infection among HIV seropositive subjects and high risk group for HIV infection in Bagmati Zone, Nepal. By: Navaraj Raj Adhikari 

227. Assessment of therapeutic of anti-mallarial drug (chloroquine) for plasmodium vivax in kanchanpur district, Nepal. By: Dhan Kumar Pant 

228. Study on intestinal infections by parasite and some bacteria among elderly people of Kathmandu Valley.By: Bikash Shakya 

229. Microbial study of hospital environment and carrier pattern study among staff in Nepal Medical College Teaching Hospital. By: Jyoti Pant 

230. Assessment of hazard analysis critical control point (HACCP) from restaurants of Kathmandu metropolitan city with respect to environmental condition. By: Poonam Thapa 

231. Sero-epidemiology of Japanese encephalitis in Nepal. By: Shyam Prasad Dumre 

232.  A study on soil transmitted helminthiasis in Kathmandu Valley. By: Arina Shrestha 

233. Study on the incidence of urinary tract infection in diabetic patients and the prevalence of multidrug resistant strains among the bacterial pathogenic isolates. By: Nisha Puri 

234. Prevalence of bacterial and fungal agents causing lower respiratory tract infections in patients with human immunodeficiency virus (HIV) infection. By: Sanchita Dahal 

235. Isolation and identifcaton of the etiolotical agent of pulmonary tuberculosis in patients visiting national tuberculosis center, Thimi, Bhaktapur. By: Sudeep Singh 

236. Microbial flora among vstors and the hospital environment in ICU and SICU at TUTH. By: Shishir Sharma 

237. A study on possible contribution of horizontal transmission in neonatal sepsis at TUTH. By: Sangeeta Shrestha 

238. Prevalence of methicillin resistant staphylococcus aureus (MRSA) in clinical specimnets from patients and screening of nasal carriage of MRSA from Medical Staffs of Bir Hospital. By: Kiran Sapkota 

239. Study of the disease citrus canker and field trial to find its effective control measure in “Kavre” Nepal.By: Dinesh Dhakal 

240. Effect of dual inoculation of Rhizobium leguminosarum biovar p[haseoli and Piriformospora indica verma et al. on phaseolus vulgaris grown in the soil treated with vermicompost. By: Jeny Shrestha 

241. Study on the effect of co-inoculation of bradyrhizobium japonicum and pirifirmospora indica verma et al. on glycine max (L.) merr. By: Rajani Shrestha 

242. A study on microbiology of urinary tract nfection at Tribhuvan University Teaching Hospital Kathmandu Nepal. By: Shova Khanal 

243. Evaluation of antibiacterial activity of some medicinal plants frequently used in respiratory and gastrointestinal diseases in Nepal. By: Olivia Thapa 

244. Pattern of bacterial flora in various out patient departments of TUTH. By: Rachana Manandhar 

245. A comparative study of different diagnostic methods for Mycobacterium tuberculosis in suspected patients visiting National Tuberculosis Centre, Thimi, Bhaktapur, Nepal. By: Asta Ram Khagi 

246. Study on prevalence of common types of vaginitis (candidiasis, traichomoniasis and bacterial vaginosis) among the pregnant women visiting thapathali maternity hospital Kathmandu. By: Sarita Shrestha 

247. Role of Glomus Microcarpum in the production of whear (triticum aestivum)  plants. By: Nirmala Dhungana 

248. Study of bacteria causing urinary tract infection and their antimicrobial resistance trend at national public health laboratory. By: Padma Shrestha 

249. Nalidxic acid resistant salmonella with decreased ciprofloxacin susceptibility. By: Rup Bahadur Kunwor 

250. Corelation of secondary infection with peripheral level T lymphocyte with CD4 marker (CD$) count in HIV/AIDS patients. By: Shiva Ram Pant 

251. A study on Microbiological and chemical quality of water of Kathmandu. By: Rama Gyawali 

252. Study on seroprevalence of IgM Antibiodies against the agents of torch infections among the patients visiting National Public Health Laboratory. By: Sujata Lamichhane 

253. Effect of dual inoculation of azotobacterchroococcum and piriformospora indica verma et al on oryza satwal croun in the soil treated with vermicompost. By: Kamil Prajapati 

254. Microbiological study on gastroenteritis of children from Kanti Children's Hospital with reference to cyclospora and rotavirus infection. By: Shradha Chipalu 

255. Comparative evaluation of microscopic and cultural examination in bacterial meningitis among the patients attending Kanti Children Hospital. By: Rojita Tuladhar 

256. Study of drinking quality of Kathmandu Metropolitan areas and evaluation of antibacterial property of some medicinal plants against isolated enteric bacteria. By: Anup Muni Bajracharya 

257. DNA fingerprinting of Mycobacterium tuberculosis isolates in Nepal using PCR-labelled is 6110 probe. By; Saraswoti Kadge 

258. Use of Loop-mediated isothermal amplification (Lamp) for direct detection of Mycobacterium in sputum. By: Bal Ram Adhikari 

259. Study of antibiotic susceptibility pattern of mycobacterium tuberculosis in pulmonary tuberculosis patients visiting national tuberculosis center, Thimim Bhaktapur, Nepal. By: Semuhang Subba 

260. Assessment of drinking water quality of madhyapur-Thimi ans study of anti bacterial effect of lime juice against bacterial isolates. By: Bina Laxmi Jayana 

261. Study the hospital environment of shahid gangalal national heart centre. By: Kamala Lamsal 

262. Study on bacteriological profile of infected wound from patient's visiting to lumbini zonal hospital, butwal, Nepal. By: Yasoda Gyawali 

263. Prevalence of bacteraemia and septicaemia among children attending kanti children hospital with special reference to salmonella spp. By: Deena Shrestha 

264. Study on intestinal parasitic infections in tharu community of bardiya district. By: Pragya Sharma 

265. Screening of mycobacterium tuberculoss by selective inhibition with para-nitrobenzoic acid, its cytochemical staining and drug susceptibility to primary anti-tubercular drugs. By: Sujaya Nepali 

266. Microbiological and physico-chemical analysis of alcoholic beverages of Kathmandu Valley. By: Bhim Shrees 

267. Study on drinking water quality of Kathmandu and attending susceptibiligy of isolates . By: Prashanna Raj Kafle 

268. Seroprevalence of rubella in Nepal. By: Khagendra Prakash K. C 

269.  Reproductive tract infections among women attending gynaecological outpatient department Tribhuvan University Teaching Hospital. By: Madan Singh Bohara 

270. Tuberculosis and human imuno-deficency virus co-infection in suspected TB patients. By: Sunita Maharjan 

271. Study of biodiversity and bioactivity of endophytic fungi of some Himalayan conifers of Nepal. By: Srijana Thapaliya 

272. Bacterial isolatres and their antibiogram from wounds and abscesses of surgical outpatients visiting bir hospital. By: Prashamsa Karkee 

273. Comparison of the resistance ratio and proportikon methods for drug susceptibility testing of Mycobacterium tuberculosis isolated from patients visiting national tuberculosis centre. By: Sushma Acharya 

274. Pattern of bacterial isolates and antibiogram from open wound infection an\mong the indoor patients of Bir Hoapital. By: Kiran Kumari 

275. Comparative study of polymerase chain reaction (PCR) and loop-mediated isothermal amplification (Lamp) for direct detection of Mycobacterium tuberculosis in sputum. By: Binita Koirala 

276. Sterid biosynthesis and embryonic stem cell proteins as putative predictive breast cancer biomarker. By: Khagendra Koirala 

277. Enteropathogenic microorganisms in children under ten years of age attending Kanti Children's Hospital. By: Sarmila Tandukar 

278. Seroprevalence of hepatitisc and HIV among blood donors in Kathmandu valley. By: Surendra Karki 

279. Prevalence of soil transmitted parasites in raw vebetables of Kathmandu and stool samples of school children. By: Anil Shrestha 

280. Estimation of incidence of HIV infection in Nepal by mode of transmissionamong various exposure groups. By: Rumika Maharjan 

281. Genetic simalasrities among bacillus thuringiensis strains from different climatic zones of Nepal. By: Nirajan Bhattarai 

282. Biochemical and molecular characterization of actinomycetes prosessing antibacterial properties from soil samples of kalapatthar, mounteverest region. By: Chiringma Sherpa 

283. Screening of actinomycetes from soil samples of Kalapatthar mount everest region for antibiosis. By: Tara Devi Gurung 

284. Immunological screening of actinomycetes of khumbu region of Nepal. By: Suman Thapa 

285. Multidrug resistance among various clinical bacterial isolates and production of different types of B-lactamases with subsequent transfer mechanism by plasmid DNA analysis. By: Pankaj Baral 

286. Isolation identification and plasmid profiling of multidrug resistant bacterial pathogens isolated from UTI patients. By: Sanjiv Neupane 

287. An evaluation of 5% NaOCI microscopy method for the laboratory diagnosis of pulmonary tuberculosis. By: Suman Lama 

288. Assessment of arsenic tolerant bacteria from arsenic contaminated groundwater in nawalparasi district of Nepal. By: Shree Krishna Shrestha 

289. Isolation and characterization of arsenic tolerant microorganisms from tube well water of Nawalparasi, Nepal. By: Prerana Dhungana 

290. Biochemical and genetic characterization of actinomycetes from  mount everest base camp. By: Manita Guragain 

291. Perspectives of arsenic exposure and asymptomatic microbial infections in Nawalparasi District. By: Narendra Maden 

292. Microbiological quality evaluation of dahi/yoghurt of Kathmandu Valley. By: Kashi Ram Ghimire 

293. Evaluation of antivicrobial activities of medicinal plants against some fungi and antibiotic resistant bacteria. By: Bishnu Prasad Marasini 

294. Urinary tract infection in diabetic microalbuminuric patients visiting B&B Hospital. By: Gridhari Rijal 

295. A comparative study of IGM capture Elisa and particle agglutination assay for the diagnosis of Japanese Encephalitis among some Nepalese patients. By: Santa Raj Khanal 

296. Study on antimicrobial activities of actinomycetes isolated from soils of different parts of khumbu region. By: Junu Koirala 

297. Estimation and projection oif the trend of HIV/AIDS in Nepal till 2010 using estimation and projection pakage (EPP) software. By: Manoj Khadka 

298. Cross-sectional study of urinary pathogens and their antibiotic susceptibility pattern with reference to extended spectreum beta lactamase (ESBL) producing strains in Kathmandu Model Hospital. By: Neelam Karna 

299. Evaluation of antibacterial activities of medicinal plants. By: Naresh Maharjan 

300. The study of antibacterial activities of common spices. By: Dinesh Maharjan 

301. Antibiotic susceptibility pattern of salmonella isolates from blood sample of patients visiting Shree Birendra Hospital, Chauni. By: Barsha Gurung 

302. Comparasion of blood culture and single slide agglutination widal test for the diagnosis of enteric fever. By: Minu K. C 

303. Bacteriological profile and antibiotic susceptibility pattern of the isolates from infected burn wound at Kanti Children's Hospital. By: Rupa Nepal 

304. Comparative evaluation of macroscopic, microscopic, serological and cultural examination of csf in bacterial memingitis. By: Nabaraj Dahal 

305. Study on HIV and sexually transmitted infections among the female commercial sex workers of Kathmandu Valley. By: Prakash Shrestha 

306. Screening of antimicrobial activity of actinomycetes from soil samples of manang region of Nepal and their biological characterization. By : Rishi Baniya 

307. Fluoroquinolone susceptibiligy pattern of the salmonella isolates from enteric fever patients visiting to National Public Health Laboratory, Nepal. By: Dhiraj Acharya 

308. Sero-epidemiology of Japanese encephalitis in some selectedhospitals of Nepal. By: Krishna Prasad Pant 

309. Sero-epidemiology of dengue virus infection in the post monsoon period I terai region of Nepal. By: Ramesh Pun 

310. Bacteriological profile of urine of postoperative patients undergone open heart surgery at Shahid Gangalal National Heart Centre, Nepal. By: Supriya Sharma 

311. Transfusion transmissible infections among blood donors in Kathmandu, Nepal. By: Ashish Chandra Shrestha 

312. Bacteriological and histological profile of heart valves resected from infective endocarditis patients. By: Sulochana Manandhar 

313. Prevalence of helicobacter pylori among dyspeptic patients attending Bir Hospital, Nepal. By: Shailaja Adhikari 

314. Isolation, identification and antibiotic sensitivity testing of salmonella serovars from enteric fever suspected patients visiting Bir Hospital. By: Manita Aryal 

315. Antibiotic susceptibility pattern of salmonella from blood of suspected enteric fever patients attending Patan Hospital. By: Krishna Govinda Prajapati 

316. Seroprevalence of hepatitis B virus among blood donors in Jhapa, Nepal. By: Hemanta Khanal 

317. Bacterioloigcal profiles of tracheal aspirates of patients attending National Institute of Neurolobical and allied sciences. By: Pratirodh Koirala 

318. Evaluation of the three commercially availavle elisa test kits for the detection of Anti- HIV antibodies. By: Avishekh Gautam 

319. Spectrum and antibiotic susceptibility pattern of bacterial isolates causing conjunctivitis among the patients visiting B.P. Koirala lions center for ophthalmic studies. By: Archana Bhattarai 

320. Cholera incidence among diarrhoeal patients visiting national public health laboratory, Nepal. By: Rabindra Karki 

321. Bacterioogy of chronic dacryocystitis and antibiotic susceptibiligy pattern of isolated bacteria. By: Anita Bhattarai 

322. Isolation and characterization of salmonella from drinking water samples of urban water supply system of Kathmandu. By: Esha Shrestha 

323. Strain typing of mycobacterium leprae isolates from Nepal uning variable number of tanden repeats. By: Pratibha Thapa 

324. Use of minisatellite genetic profiling with clinical analysis of leprosy patients in Nepal. By: Binita Adhikari

Source: Microbiological Abstracts, Published by MISAN, Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.

Advice for potential biology graduate students

There are a few things to keep in mind before you apply for graduate course in biology. First, be realistic about graduate school. Graduate school in biology is not a sure path to success. Many students assume that they will eventually get a job just like their advisor's. However, the average professor at a research university has 3 students at a time for about 5 years each. So, over a career of 30 years, this professor has about 18 students. Since the total number of positions has been pretty constant, these 18 people are competing for one spot. So go to grad. school assuming that you might not end up at a reserach university, but instead a teaching college, or a government or industry job. All of these are great jobs, but it's important to think of all this before you go to school.
Second, choose your advisor wisely. Not only does this person potentially have total control over your graduate career for five or more years, but he/she will also be writing recommendation letters for you for another 5-10 years after that. Also, your advisor will shadow you for the rest of your life. People will always think of you as so-and so's student and assume that you two are somewhat alike. Finally, in many ways you will turn into your advisor. Advisors teach very little, but instead provide a role model. Consciously and unconciously, you will imitate your advisor. You may find this hard to believe now but fifteen years from now when you find yourself lining up the tools in your lab cabinets just like your advisor did, you'll see. Someone once said that choosing an advisor is like choosing a spouse after one date. Find out all you can on this date.

Finally, have your fun now. Five years is a long time when you are 23 years old. By the end of graduate school, you will be older, slower, and possibly married and/or a parent. So if you always wanted to walk across Nepal, do it now. Also, do not go to a high-powered lab that you hate assuming that this will promise you long term happiness. Do something that you have passion for, work in a lab you like, in a place you like, before life starts throwing its many curve balls.

If, after reading this, you still want to apply for grad study, apply now.

Concepts in Biology: Laboratory Manual