Most people who have a balanced translocation have the right amount of chromosome material but it has been rearranged in some way. This may happen if two chromosomes swap pieces (a reciprocal translocation). In other cases two whole chromosomes may become stuck together (a Robertsonian translocation). This page describes what happens when someone has a reciprocal translocation.

Reciprocal chromosomal translocations occur following double-strand breaks (DSBs) in DNA when a section of one chromosome is exchanged with that of another, non-homologous chromosome. These exchanges may produce a dysfunctional fusion gene that disrupts cell growth and survival pathways, such as the translocations seen in leukemia and childhood sarcomas.

Chromosomal translocations have been well studied in cancer cell lines which are associated with two types of cancer, acute myeloid leukemia and Ewing's sarcoma, but determining how they contribute to cancer development is complicated by additional mutations and altered gene expression profiles in these cultured cells. Now, Juan Carlos Ramirez, head of the Viral Vector Facility at the Fundacion Centro Nacional de Investigaciones Cardiovasculares (CNIC) and his colleagues Raul Torres at CNIC and Sandra Rodriguez-Peralez at the Spanish National Cancer Center (CNIO) in Madrid, Spain have used a new genome editing tool, CRISPR-Cas9, to induce chromosomal translocations for the first time in a human cell line and in primary cells. The study's authors conclude by stating that the use of this technology will allow for the clarification of how and why chromosomal translocation occurs, which without doubt will allow new anti-cancer therapeutic strategies to be tackled.

Using RNA-Guided Endonuclease (RGEN) technology or CRISPR/Cas9 genome engineering technology, CNIO and CNIC researchers have shown that it is possible to obtain such chromosomal translocations. The CRISPR-Cas9 system is extremely simple to introduce a cut at the desired locus, easier to design, and cheaper than many other systems. Using the CRISPR-Cas9 system, Ramirez and his colleagues reproduced the translocations observed in Ewing’s Sarcoma (ES) and Acute Myeloid Leukemia (AML) patient cell lines in HEK293 cells and also generated the ES translocation in human mesenchymal stem cells and the AML translocation in umbilical cord blood cells.

By focusing on chromosomal translocation without the confounding characteristics of established cell lines, these new cells lines should help answer the fundamental question of what causes a cell to become cancerous. Ramirez and his team now look forward to modeling other chromosome translocations in a variety of cell types.

Reference:

http://en.wikipedia.org/wiki/Chromosomal_translocation

http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

Brief description: We are looking for suitable candidates in the area o computational biology/bioinformatics/genomics or related field for next-generation sequencing (NGS) data analysis for small-RNAs, RNA-Seq and targeted resequencing of plants and associated organisms. We are an interdisciplinary group where projects equally involve bioinformatics and systems biology (specially microarrays and next-generation sequencing (NGS) data analysis and its use), along with plant molecular biology, genetic engineering, field biology, and analytical plant chemistry for understanding response of plants to biotic stresses.

Essential qualification: MSc/BTech/MTech/PhD (or other suitable qualification) in disciplines preferable to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance Post-Graduate Diploma in Bioinformatics’. Proficiency in programming languages (such as Perl, C++) and/or statistics (proficient in R for example) is compulsory.

Desirable qualification: Experience in the field of genomics e.g. microarray analysis, NGS, genome annotation, database development and management, software development, systems and network biology (or related fields) will be preferred.

Application process: Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by e-mail to Shree Prakash Pandey, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, WB, India within 14 days of this advertisement.

E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in

Advertisement:

http://www.iiserkol.ac.in/announcements/adverts/671-advt_ra_shree_prakash_july_2014

Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can make specific classifications, exploiting point mutations to distinguish close taxa. AA-based classifiers have higher sensitivity in detecting homology between query and reference sequences, leverageing higher conservation of AA sequences. Metabuli combines the information of both sequence types using a novel k-mer structure, metamer, to enable both specific and sensitive characterization of metagenomic samples. In addition, it can classify reads against a database of any size as long as it fits in the hard disk.

Address of the bookmark: https://github.com/steineggerlab/Metabuli

Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes — a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population. 

The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.

Reference:

http://www.pnas.org/content/111/Supplement_3/10796.full

Image : http://i.kinja-img.com

Bdelloid rotifers are small animals well known for their ability to survive in harsh conditions. They can endure extreme dehydration by entering a state of dormancy and then revive when water becomes available again. Scientists have always been interested in the degree to which these animals resist radiation, since radiation can severely damage DNA by causing both of its strands to break. Interestingly, Adineta vaga's ability to survive radiation may be connected to the way in which it tolerates drying out, as dehydration can also damage DNA. The rotifer probably evolved strong DNA protection and repair mechanisms primarily as a response to its severe environment. Its resistance to radiation is merely a byproduct of adapting to the cycles of drying and rehydration.

In order to find out more about this ability, the researchers subjected A. vaga to proton radiation and then examined what effect it had on its chromosomes. The radiation caused serious damage, resulting in hundreds of breaks in the DNA. For the vast majority of organisms, such extensive chromosome damage would be disastrous; it's similar to going through an instruction manual in a shredder and ending up with a large number of separate fragments. The scientists believed that the rotifers would repair their chromosomes before producing offspring. However, what they discovered was unexpected: some of the broken pieces of chromosome did survive and were passed on to the next generations, where the repair process continued.

The discovery took on even greater interest when the scientists examined the offspring of the irradiated rotifers. Rather than observing the same DNA damage in all the generations, they found different sized sections missing and evidence that some of the genetic regions which had been lost were being slowly restored. The researchers proposed that the rotifers use a repair mechanism known as Break-Induced Homologous Extension Repair, or BIHER. In simple terms, a broken piece of DNA can locate a matching sequence on the other chromosome and use it as a guide to rebuild itself. If the damage is beyond what can be repaired in one generation, the repair process can continue in the next.

What makes the rotifer's method of repairing DNA so unusual is that, normally, we consider DNA repair to take place immediately after damage has occurred, with the cell rapidly repairing the damaged DNA. In A. vaga, however, the repair process can be a lot longer. Certain pieces of chromosome survive the initial damage, are inherited, and then serve as the basis for further repairs in later generations. It's as if one generation begins mending a broken book, the next one continues the work, and another eventually completes the job until all the missing parts have been restored.

One reason why this might work is that bdelloid rotifers have holocentric chromosomes. Rather than having a single point, as most chromosomes do, which controls movement during cell division, the ability to move is distributed along the entire length of their chromosomes. As a result, fragments of chromosomes are sometimes able to retain the parts that are necessary for them to move and divide, and this may account for how broken pieces of chromosome can last long enough to be passed on and then repaired.

This finding could have implications that go beyond those concerning rotifers. Scientists are interested in understanding how genomes cope with severe chromosome damage, for example in the case of chromothripsis, where chromosomes break and are then reassembled in new configurations. Investigating A. vaga could help us to learn how cells manage large genetic issues. Moreover, its high resistance to radiation might also prove useful in research into extreme environments, such as the radiation hazards encountered on long space missions. However, these are ideas for future investigation; at present the rotifer's DNA repair mechanism cannot be used to protect people from radiation.

What is perhaps the most interesting aspect of this discovery is that the rotifer's remarkable ability could have developed for a very simple reason. Since an animal living in moss constantly undergoes periods of drying out and then getting wet again, the same mechanisms that protect its DNA when it is dehydrated might also enable it to survive radiation which would damage most other animals. Therefore, the rotifer probably did not evolve solely in order to resist radiation; instead, it became extremely good at coping with the difficult conditions it encounters, and radiation resistance was just a byproduct.

The case of Adineta vaga demonstrates that survival does not always mean avoiding damage; on some occasions it involves being able to recover from damage which appears to be impossible to repair. This small animal can survive having its chromosomes broken into many pieces, retain some of those pieces, pass them on to its offspring, and continue to repair them over successive generations. Although we generally regard DNA as something fragile that must always remain intact, the rotifer indicates an alternative possibility: perhaps a genome does not have to be perfect in order to survive, since sometimes the pieces last long enough for life to reassemble them, bit by bit, generation after generation.

Ream more at https://www.science.org/doi/10.1126/sciadv.aee0891

Address of the bookmark: https://peerj.com/preprints/453.pdf

https://biosciences.hs-mittweida.de/equant/

Address of the bookmark: https://biosciences.hs-mittweida.de/equant/

ROLLING ADVERTISEMENT NO. 01/2014(E-1)
ADVERTISEMENT FOR THE POSITIONS OF ASSISTANT PROFESSOR CANDIDATES CAN APPLY ANY TIME DURING THE YEAR.

IIT Delhi invites applications from qualified Indian Nationals, Persons of Indian Origin (PIOs) and Overseas Citizens of India (OCIs) for the following positions in the various Departments/Centres/Schools (in the fields
mentioned alongwith them):
Post Pay Band Assistant Professor and Assistant Professor (on Contract) Rs.15600-39100 (PB-3) (Minimum pay of Rs.30000/-)+ AGP Rs.8000/-

The following norms will be followed for fixing the basic pay + AGP for Assistant Professors appointed on
contract with Ph.D but experience of 3 years or less:-
Type Qualification & Experience on the date of joining
Assistant Professor (Contract) PB3 (Rs. 15,600-39,100).

MINIMUM QUALIFICATIONS AND EXPERIENCE:
Ph.D. with First class at the preceding degree or equivalent in the appropriate branch with very good academic record throughout. A minimum of three years industrial/research/teaching experience, excluding however, the experience gained while Pursuing Ph. D. The candidates should preferably be below
35 years of age for male and 38 years for female ( to be relaxed by 5 years in case of persons with physical disability, SC/ST and 3 years in case of OBC-NCL).

Qualified persons include:
(a) Indian Nationals,
(b) Foreign Nationals who are “Persons of Indian Origin” (PIO) or Overseas
Citizens of India (OCI), in whose case, if selected, permission will be sought from Govt. of India
before he/she can join IIT Delhi, or
(c) Other Foreign Nationals, in whose case, if selected, appointment will be on a contract basis for up to 5 (five) years subject to permission from the Govt. of India before he/she can join IIT Delhi.
(d) Institute specifically encourages applicants from SC/ST/OBC category as well as persons
with disability to apply for these positions.

AMAR NATH & SHASHI KHOSLA SCHOOL OF INFORMATION TECHNOLOGY:
Computational Neuroscience, Medical Applications of Information Technologies, Computational & Systems Biology, Machine to Machine (M2M) Technologies, Embedded Systems & Sensors, Computer Security.
KUSUMA SCHOOL OF BIOLOGICAL SCIENCES:
In-silico Biology Applications, Systems Biology, Infection Biology, Neurodegeneration.

More at http://www.iitd.ac.in/sites/default/files/jobs/faculty/spl-areas-rolling-advt.pdf

http://www.iitd.ac.in/content/faculty-positions