More at http://clark.genetics.utah.edu/

Our research centres on the use of genetics/genomics and phenotypic studies to address complex questions in the ecology, epidemiology and evolution of microbes. Our most recent interest focuses upon comparative genome analysis to describe the core and flexible genome of pathogenic bacteria (Campylobacter, Acinetobacter, Escherichia coli, Helicobacter, Staphylococcus and Streptococcus suis) and how this is related to population genetic structuring, the maintenance of species, and the evolution of host/niche adaptation and virulence.

More at https://sheppardlab.com/research/

Key Findings:

1. Chromosomal Fusion and Its Molecular Signature:

   • The fusion site is located at 2q13–2q14.1 and is characterized by degenerate telomeric sequences appearing interstitially, indicating the historical head-to-head joining of ancestral chromosomes.
   • Despite being a signature of a past fusion event, these telomeric repeats are no longer functional and have undergone sequence degradation over time.

2. Extensive Duplications in the Surrounding Genomic Region:

   • The study identifies large-scale segmental duplications flanking the fusion site, with several of these regions duplicated and scattered across multiple chromosomes.
   • These duplications are predominantly located in subtelomeric and pericentromeric regions, suggesting their role in genomic instability and chromosomal evolution.

3. Paralogous Regions and Their Evolutionary Relationships:

   • A 168-kilobase (kb) segment near the fusion site has 98%–99% sequence identity with three regions on chromosome 9 (9pter, 9p11.2, and 9q13).
   • Another 67-kb region distal to the fusion site shows a high degree of homology to sequences in chromosome 22qter.
   • Additionally, a 100-kb segment exhibits 96% sequence identity with a region in chromosome 2q11.2.

4. Comparative Genomics and Evolutionary Implications:

   • By comparing the duplicated sequences and their arrangement in primates, the researchers traced the order of duplication events leading to their present distribution.
   • The presence of specific repetitive elements within these duplicated segments serves as evolutionary markers that help infer their historical rearrangements.
   • Some of these duplicated regions are associated with chromosomal inversion breakpoints, potentially contributing to evolutionary changes in primates.
   • Recurrent structural rearrangements in these regions have been linked to human chromosomal disorders.

Conclusions and Implications:

• The findings provide valuable insights into the structural evolution of human chromosome 2, which played a crucial role in human speciation.
• Understanding these segmental duplications and their evolutionary trajectories sheds light on genomic instability, which may contribute to human genetic diseases.
• The study highlights how large-scale chromosomal rearrangements, such as fusion and duplication, have influenced the evolutionary divergence of humans from other primates.

This research advances our understanding of human genome evolution and offers a foundation for studying the effects of structural variants in genetic disorders.

Key Findings of the Study:

1. Alu Insertion and Tail Loss:
   The researchers discovered an Alu-mediated genetic change in a common ancestor of modern apes and humans. This change disrupted the normal function of a gene involved in tail development, leading to the suppression of tail formation.

2. Gene Disruption Mechanism:
   The Alu insertion was found within a regulatory region of the TBXT gene (also known as T or Brachyury), which is crucial for tail development in vertebrates. This insertion likely altered the gene's expression patterns, leading to tail reduction over evolutionary time.

3. Functional Evidence from Model Organisms:
   To test their hypothesis, the researchers introduced similar genetic modifications in mice. The modified mice exhibited shortened or absent tails, supporting the idea that the identified mutation played a role in tail loss in hominoids.

4. Evolutionary Implications:
   The findings suggest that small, random genomic changes—such as transposable element insertions—can have profound effects on body morphology. This study provides evidence that mobile DNA elements (like Alu) can drive major evolutionary transitions.

5. Relevance to Human Evolution:
   Understanding the genetic basis of tail loss helps in reconstructing the evolutionary history of hominins (the lineage that includes humans and our extinct relatives). It also sheds light on how genetic variations contribute to anatomical diversity among primates.

Significance of the Study:

This research highlights the role of transposable elements in shaping evolutionary traits and provides a concrete genetic explanation for a defining characteristic of humans and great apes. It also demonstrates how mutations in regulatory regions of developmental genes can lead to significant anatomical changes.

Address of the bookmark: http://chmille4.github.io/Scribl/

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

Address of the bookmark: https://gvolante.riken.jp/

• Using state of the art tools, easily extended for other viruses

• Tool and database updates for critical components via Conda

• Built using modern design patterns with Conda and Snakemake

• Extensible and easy to customize

• Submission Ready Genomes

• Customizable reporting with comprehensive visualization

https://ikim-essen.github.io/uncovar/

Github https://github.com/IKIM-Essen/uncovar

Address of the bookmark: https://ikim-essen.github.io/uncovar/

Translational recoding.

RNA editing.

Evolution of the genetic code and translation.

More at http://lapti.ucc.ie/research.html

Lab page http://lapti.ucc.ie/index.html

The ongoing 2014 West Africa Ebola outbreak is considered to be the largest and longest outbreak ever recorded of Ebola, killing at least 932 people and infecting more than 1,700 till date since March in Sierra Leone, Guinea, Nigeria and Liberia.

Hence, the World Health Organisation (WHO) on 8 August, 2014 declared the killer Ebola epidemic ravaging parts of West Africa an international health emergency.

Causes

EVD is caused by infection with a virus of the family Filoviridae, genus Ebolavirus. While there are five identified sub-species of Ebolavirus, four viruses cause disease in humans. They are Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), Taï Forest virus (TAFV).

The fifth virus, Reston virus (RESTV), is not considered to be disease-causing in humans.

According to WHO, EVD first appeared in 1976 in two simultaneous outbreaks, in Nzara, Sudan, and in Yambuku, Democratic Republic of Congo. The latter was in a village situated near the Ebola River from which the disease takes its name.

How does it spread?

It is still unclear how Ebola spreads. However, it is believed that the first pateint becomes infected through contact with an infected animal's body fluids.

Human-to-human transmission can occur through direct contact with blood, organs or other body fluids of infected people or exposure to objects such as needles and syringes that have been contaminated with infected secretions.

Ebola can also be transmitted from men who have recovered from the disease through semen as it is infectious for up to 7 weeks.

Infected dead bodies can spread Ebola as they are still infectious. So mourners who have direct contact with the body of deceased person can also get the disease.

Who is most at risk?

Health-care workers who do not wear appropriate protective clothing and family members who are in close contact with infected people or deceased patients.

Signs and symptoms:

Symptoms may occur between 2 and 21 days after contracting the infection. Common signs of Ebola include:

Fever

Headache

Muscle, abdominal and joint pain

Sore throat

Weakness

Diarrhea

Vomit or cough up blood

Chest pain

Difficulty in breathing and swallowing

Rash

Hiccups

Bleeding inside and outside the body

Prevention

Currently there is no vaccine available for humans. But the infection can be controlled through the use of recommended protective measures such as:

Avoid contacting infected blood or secretions, including from those who are dead .

Using standard precautions for all patients in the healthcare setting.

Sterilizing equipment, and wearing protective clothing including masks, gloves, gowns and goggles.

Washing your hands with soaps or detergents.

Disinfecting your surroundings.

Isolate people who have Ebola symptoms.

Culling of infected animals, with close supervision of burial or incineration of carcasses.

Yet, not travelling to the areas or countries where the virus is found is the best way to avoid Ebola.