Lifeboat Foundation

Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven “Baltimore classes” (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.

Scientists at Uppsala University have proposed an addition to the theory of evolution that can explain how and why genes move on chromosomes. The hypothesis, called the SNAP Hypothesis, is presented in the scientific journal PLOS Genet ics.

Life originated on Earth almost 4 billion years ago and diversified into a vast array of species. How did this diversification occur? The Theory of Evolution, together with the discovery of DNA and how it replicates, provide an answer and a mechanism. Mutations in DNA occur from generation to generation, and can be selected if they help individuals to adapt better to their environment. Over time, this has led to the separation of organisms into the different species that now inhabit all ecosystems.

Current theory holds that evolution involves mistakes made when replicating a gene. This explains how genes can mutate over time and acquire new functions. However, a mystery in biology is that the relative locations of genes on chromosomes also change over time. This is obvious in bacteria, as different species often have the same genes in very different relative locations. Since the origin of life, genes have apparently been changing location. The questions are, how and why do genes move their relative locations?

An international team of researchers that pooled genetic samples from developmentally disabled patients from around the world has identified dozens of new mutations in a single gene that appears to be critical for brain development.

“This is important because there are a handful of genes that are recognized as ‘hot spots’ for mutations causing neurodevelopmental disorders,” said lead author Debra Silver, an associate professor of molecular genetics and microbiology in the Duke School of Medicine. “This gene, DDX3X, is going to be added to that list now.”

An analysis led by the Elliott Sherr lab at the University of California-San Francisco found that half of the DDX3X mutations in the 107 children studied caused a loss of function that made the gene stop working altogether, but the other half caused changes predicted to disrupt the function of the gene.

This month, K.L. became one of the first patients to receive a new experimental gene therapy for children with a severe form of inherited vision loss. The treatment, currently not yet named, targets young men who are susceptible to a particularly vicious genetic disorder that gradually destroys the light-sensing portion of their eyes.

Within a month following a single injection, “my vision was beginning to return in the treated eye. The sharpness and depth of colors I was slowly beginning to see were so clear and attractive,” said K.L.

The trial, a first-in-human case for X-linked Retinitis Pigmentosa (RP), was led by Dr. Robert MacLaren at the University of Oxford but spanned multiple centers including the Bascom Palmer Eye Institute in Miami, which previously championed Luxterna, the first FDA-approved gene therapy for a type of inherited blindness. The results are some of the first targeting a particularly difficult gene prone to mutation in humans. Amazingly, despite some inflammation in early stages, the therapy provided massive improvements in eyesight as early as two weeks following treatment.

Is it so outlandish to believe that countries in the future might resort to military force to prevent other countries from altering the shared genetic code of humanity? Many countries have been invaded for far less.

The genetics revolution that will transform our health care, the way we make babies, the nature of the babies we make, and ultimately our evolutionary trajectory as a species has already begun. Just like parents in many places will need to make tough choices about whether, if at all, to genetically engineer their children, states will be forced to make monumental collective decisions on these issues with potentially fateful consequences.

Continue reading “The designer baby debate could start a war” »

The gene-editing tool CRISPR has been used for the first time inside the body of an adult, in an attempt to cure a form of blindness.

The treatment: According to the Associated Press, doctors dripped just a few drops of a gene-editing mixture beneath the retina of a patient in Oregon who suffers from Leber congenital amaurosis, a rare inherited disease that leads to progressive vision loss.

Cells that take up the mixture can have their DNA permanently corrected, potentially restoring a degree of vision.

CRISPR Used To Edit Genes Inside A Patient With A Rare Form Of Blindness : Shots — Health News Doctors used CRISPR to edit genes of cells inside a patient’s eye, hoping to restore vision to a person blinded by a rare genetic disorder. A similar strategy might work for some brain diseases.

Domestic cats exhibit abundant variations in tail morphology and serve as an excellent model to study the development and evolution of vertebrate tails. Cats with shortened and kinked tails were first recorded in the Malayan archipelago by Charles Darwin in 1868 and remain quite common today in Southeast and East Asia. To elucidate the genetic basis of short tails in Asian cats, we built a pedigree of 13 cats segregating at the trait with a founder from southern China and performed linkage mapping based on whole genome sequencing data from the pedigree. The short-tailed trait was mapped to a 5.6 Mb region of Chr E1, within which the substitution c. 5T C in the somite segmentation-related gene HES7 was identified as the causal mutation resulting in a missense change (p. V2A). Validation in 245 unrelated cats confirmed the correlation between HES7-c. 5T C and Chinese short-tailed feral cats as well as the Japanese Bobtail breed, indicating a common genetic basis of the two. In addition, some of our sampled kinked-tailed cats could not be explained by either HES7 or the Manx-related T-box, suggesting at least three independent events in the evolution of domestic cats giving rise to short-tailed traits.

The majority of vertebrate species, with the remarkable exceptions of humans and apes, possess a visible tail throughout their lifespans. The animal tail is an important appendage to the torso and plays adaptive roles in locomotion, balance, communication, thermoregulation and even energy storage¹. In vertebrates, tails vary dramatically in color, size, shape and mobility and represent different evolutionary histories, including multiple independent events of shortening or loss of the tail in distinct lineages. Understanding the genetic causes of intraspecific tail length polymorphism would be one essential step toward elucidating the mechanisms underlying the development and evolution of tails. In laboratory mice, genetic studies of axial skeleton development have identified multiple genes and mutations involved in caudal vertebra development that have pleiotropic effects on fertility, somitogenesis, and meiotic recombination, thus shedding light on vertebrate evolution^2,3,4,5.

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines — such as anthropology, archaeology, linguistics and genetics — that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise.