Showing posts with label biyoloji. Show all posts
Showing posts with label biyoloji. Show all posts

Wednesday, June 8, 2022

Virüslerin Çoğu Faydalıdır



Birçok insan için ilk duyulduğunda çok ters gelse de çoğu virüs insanlar için iyidir. Vücudu-
muzda kendi hücrelerimizden daha çok bakteri olduğunu duymuşsunuzdur. Ancak bağırsaklarımızdaki bakterilerden çok daha fazla virüs olduğu da doğrudur! Aslında, bu virüs topluluğu ("virome" olarak adlandırılır)? hikmetsiz olmayıp vücudunuzdaki bakteri sayısını ve türlerini düzenlemede önemli bir rol oynar. Bu virüsler olmasaydı bağırsaklarımızda yaşayan milyarlarca aç bakteri, hızla ölümümüze sebep olabilirdi.

Hiç okyanusta yüzmeye gittiniz mi? Aslında okyanus suyu çok çeşitli türleriyle konsantre bir bakteri çorbasıdır. Ancak tıpkı bağırsağınızda olduğu gibi orada da bakterilerden daha fazla virüs vardır ve muhtemelen bu virüsler, okyanus sularındaki bakteri popülasyonunu korma ve dengelemede rol oynarlar. Virüsler olmasaydı acaba denizlerde balk bulabilecek miydik? Bu, bilim insanlarının cevap araması gereken ilginç bir sorudur.

Hiç bir gölde yüzmeye gittiniz mi? Burası da bakteri ve virüslerden olusan bir çorbadır. Gölde yüzen ördek, kuğu veya kazlarla beraber grip virüsleri de bol miktarda bulunmaktadır. İşte aslında bu su kuşları, insanlara bulaşmayanlar da dâhil olmak üzere muhtemel bütün grip virüsü türlerini taşır. Bu virüsler kuşların dışkılarıyla suya karışır. Ancak genellikle bu kuşlarda hastalık üretmediği gibi, yüzen insanların da gözlerinden, kulak, burun ve ağızlarından girse bile, normal şartlarda insanda da hastalık yapmazlar.

Kuşların (genellikle) hasta olmamalarının sebebinin, virüslerle milyonlarca yıldır savaşmış olmaları ve kuşların immün sistemleriyle tanışıp âdeta bir ateşkes düzenlemiş oldukları söylenebilir. Ancak İlahî hikmetler açısından bakıldığında, grip virüsünün muhtemelen kuşlar için henüz keşfedemediğimiz faydalı bir rolü de olabileceği düşünülmelidir.

İrfan Yılmaz, Çağlayan Dergisi, Haziran 2022

Wednesday, September 15, 2021

Inside Our Body

 

Lucy Jones, Lithub

Inside your body, there are probably more microbial cells than human cells. Symbiotic organisms colonize various areas of the body—the mouth, skin, vagina, pancreas, eyes and lungs—and many reside in the gut microbiota. You almost certainly have microscopic mites living on your face in the hundreds, or even thousands—mating, laying eggs and, at the end of their lives, exploding, unbeknown to you.

You may have heard the incredible fact that the resident microbes in your body outnumber your own human cells ten to one. That figure has been downgraded to three to one or an equal number, which is still astonishing. They mostly resemble mini jumping beans or Tic Tacs on a much smaller scale. These organisms aren’t simply parasitic freeloaders: they are intricate networks that intertwine and interconnect, influencing our health and well-being through complex ecological processes. They are involved in the workings of the immune system, the gut-brain axis, protection against harmful organisms and, indirectly, they have some relationship to our mental health.

When we breathe, we suck different species of microorganisms into the body. Studies suggest 50 different species of mycobacteria would be normal in the upper airways of healthy individuals, making their way into the teeth, oral cavity and pharynx. The environment around you might look clear and empty, but it will be swarming with microscopic organisms, depending on where you are.

Our microbiota are healthiest when they are diverse—and a diverse microbiota is influenced positively by an environment filled with organ­isms, which are found more abundantly in outside spaces than inside. We imagine our skin and our bodies to be armored, or a shell impenetrable to the outdoors, that we have somehow transcended our biological origins. But the human epidermis is more like a pond surface or a forest soil, as Paul Shepard, the late American environmentalist, suggested. Even if we don’t yet understand or know exactly how many of the abundant micro­organisms in our bodies arrived with us through exposure to nature—and, indeed, how they affect our mental and physical health—we are woven into the land, and wider ecosystems, more than we realize.

Crucially, these “old friends” that we have evolved with are able to treat or block chronic inflammation. There are two types of inflamma­tion: the good, normal, protective type, whereby the immune system fires up to respond to an injury, with fever or swelling or redness; then there is the chronic, systemic kind you don’t want. This is the simmering, low-level constant inflammation within the body which can lead to cardiovas­cular disease, inflammatory disorders, decreased resistance to stress and depression. This kind of raised, background inflammation is common in people who live in industrialized, urban environments and is associ­ated with the unhealthy habits of the modern world: our diets, poor sleep, smoking and alcohol consumption, stress and sedentary lifestyles. As we age, our bodies become more inflamed. Scientists can measure levels of inflammation by looking at biomarkers such as proteins in the blood.

It should be no surprise, then, to learn that the gut microbiota of people who live in urban areas and developed countries are less biodi­verse than those who still have profound contact with the land, such as hunter-gatherers and traditional farming communities.

Scientists are starting to understand more deeply the role inflamma­tion may also play in our mental health. Evidence that bodily inflammation can affect the brain and have a direct effect on mood, cognition and behavior is relatively new. But it is strong and compelling. Depres­sion may well be all in the mind, the brain and the body. This view runs counter to the dominant view of Western medicine that our bodies and minds are separate and thus should be treated apart from each other, a view dating back to 17th-century French philosopher René Des­cartes’ concept of dualism. As the neuropsychiatrist professor Edward Bullmore has said, “In Britain in 2018, the NHS is still planned on Car­tesian lines. Patients literally go through different doors, attend different hospitals, to consult differently trained doctors, about their dualistically divided bodies.”

But perhaps we are not as dualistically divided as the Cartesian orthodoxy our health systems are still built on would lead us to believe. A study of 15 thousand children in England found that those who were inflamed at the age of nine were more likely to be depressed a decade later, as 18-year-olds. People with depression, anxiety, schizophre­nia and other neuropsychiatric disorders have been found to have higher levels of inflammation biomarkers. European people have higher levels of cytokines in the winter months, which is also a time of increased risk of depression. Levels of cytokines are higher in sufferers of bipolar disorders during their manic episodes, and lower when they’re in remission. Early findings suggest anti-inflammatory medicines may improve depressive symptoms. People with a dysregulated immune system are more likely to have psychiatric disorders.

In his book The Inflamed Mind, Bullmore argued that some depres­sions may be a symptom of inflammatory disease, directly related to high levels of cytokines in the blood, or a “cytokine squall,” as he puts it.

Could our lack of contact with the natural world be a contributing factor to high levels of inflammation, which could be related to depres­sion and other mental health disorders? Studies show that just two hours in a forest can significantly lower cytokine levels in the blood, soothing inflammation. This could partly be caused by exposure to important microorganisms.

There are multiple reasons why babies born in the rich, developed world have a less diverse population of mycobacteria—for example, the use of antibiotics, diet, lack of breastfeeding and reduced contact with the natural environment. We live inside, often in air-conditioned buildings cleaned with antibacterial sprays, with reduced exposure to organisms from the natural environment via plants, animals and the soil. Our food is sprayed and wrapped in plastic. We don’t live alongside other species of animals, as we did for millennia. The opportunities to be exposed to diverse microorganisms are much fewer—which might explain why my daughter liked to eat soil.






Thursday, September 13, 2018

Dogs are wolf at heart



It’s in the Neolithic, when humans start to farm, that dogs also start to spread beyond Eurasia for the first time. And they track the spread of farming. Dogs appear in sub-Saharan Africa after the beginning of the Neolithic there, 5,600 years ago, and take another 4,000 years to reach South Africa. Dogs appear in archaeological sites in Mexico around 5,000 years ago, coinciding with the first farmers there, but only reach the southernmost tip of South America 4,000 years later. Studies of mitochondrial DNA suggested that all those early American dog lineages were completely replaced, following the European colonisation of the Americas. But the latest genome-wide studies tell a different story: European dogs – arriving with colonisers in just the last 500 years – mixed with the indigenous New World dogs.

The modern breeds that we know so well take much longer to arrive. They are very recent inventions. Dog genes reflect this history. There are signs of two prominent genetic bottlenecks amongst the ancestors of dogs: one at the origin of domestication, and another when modern breeds emerged, in just the last 200 years. Breeders began to focus closely on promoting particular traits, producing dogs that were wonderfully obedient, providing invaluable help with hunting and herding. But the malleability of characteristics under selective breeding became an allure in itself, and so dogs were also bred with specific shapes, sizes, colours and textures. The morphological variety amongst modern dog breeds exceeds that in the whole of the rest of the family Canidae, which includes foxes and jackals as well as wolves and dogs.

There are nearly 400 breeds of dogs today, and most of them – in all their wonderful diversity – have really only been around since the nineteenth century. This is when the strict breeding needed to create and conserve the kinds of strains recognised by kennel clubs really got going. The breeds that appear to be most ancient, with the most deep-rooted lineages on the dog family tree, are actually found in places where dogs only arrived relatively recently. Dogs arrived in the islands of south-east Asia 3,500 years ago and in South Africa around 1,400 years ago and yet these areas are home to a number of ‘genetically ancient’ breeds: basenjis, New Guinea singing dogs and dingoes. This pattern shows that these lineages have been isolated for longer than most other breeds. The deep roots don’t mean that their lineages were the first to branch off, but rather that out on the periphery they have stayed the most genetically distinct.
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Lots of breeds with supposedly ancient roots, however, turn out to be recent recreations. Wolfhounds were, as their name suggests, used to hunt their wild cousins – very successfully. By 1786 there were no wolves left in Ireland, and so no need for wolfhounds. By 1840, the Irish wolfhound had also gone extinct. But then a Scotsman living in Gloucestershire, Captain George Augustus Graham, resurrected the ‘Irish wolfhound’ by breeding what he thought was a wolfhound of some kind with Scottish deerhounds. Today’s population of Irish wolfhounds comes from a very small group of ancestors so that, like many breeds, they are inbred. And while this helps to maintain the characteristics of the breed, it also increases the risk of particular diseases with a strong genetic component. Around 40 per cent of Irish wolfhounds suffer from some form of heart disease, and 20 per cent from epilepsy. They’re not the only pedigree with problems. Many dog breeds plummeted to near-extinction in the twentieth century, during the world wars, and were resurrected by outbreeding with other types of dog. Very strict breeding since then has produced extremely inbred populations, with little genetic diversity within breeds and an increased risk of diseases – ranging from heart disease and epilepsy, to blindness and particular cancers. Specific breeds are predisposed to certain afflictions: Dalmatians have a high risk of deafness; Labradors often suffer from hip problems; cocker spaniels are prone to developing cataracts.
Breeds may be relatively reproductively isolated now, but their genes tell us that there was once plenty of gene flow between breeds or proto-breeds. Breeds from separate countries share characteristics and genes which show that they must have interbred in the past. The Mexican hairless dog and the Chinese crested dog share hairlessness and missing teeth and in both breeds these traits are caused by precisely the same mutation in a single gene. The odds against this gene mutating in exactly the same way in two different dog populations are infinitesimally small. Instead, these shared traits and shared genetic signature speak of common ancestry. Dachshunds, corgis and basset hounds all have very short legs. Together with sixteen other dog breeds, they all have exactly the same genetic signature associated with this form of dwarfism – the insertion of an extra gene. It’s most likely that this insertion happened just once, in early dogs, long before any of the modern short-legged breeds appeared.

Genetic research provides us with this astonishing opportunity to understand the evolutionary history of dogs, from the pleiotropic exuberance of variety produced by selecting tameness, right through to the selection of peculiar features, suited to very particular tasks, in our modern breeds. We can see how certain mutations, and the traits associated with them, popped up amongst early dogs, and were later – much later – promoted and propagated by selective breeding to create the modern breeds we know today. With inbreeding producing problems with increased risk of disease, geneticists are also working to understand the basis of particularly prevalent diseases and it may be possible to reduce that risk by even more careful selective breeding, and judicious outcrosses, underpinned by genotyping.

Some breeds have been outcrossed beyond the bounds of domestic dogs. Such extreme outcrossing was the basis of the Saarloos wolfdog, created in 1935 by breeding together a male German shepherd with a female Eur
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Hybrid wolf-dogs have attacked and killed a number of children in the US, and are banned outright in some states. In others, wolf-dog hybrids are legal, as long as the hybridisation happened at least five generations ago. In the UK, a first- or second-generation wolf-dog hybrid is considered risky enough to be regulated by the Dangerous Wild Animals Act – the same law governing owning a lion or tiger. It seems odd that breeders would exaggerate the wolf content of their puppies – but wildness is part of the cachet of these animals. With buyers seeking ‘high-content’ and ‘wild looks’, and willing to part with £5,000 to feel more like Jon Snow, wolf-dog hybrids are big business. It’s difficult to know just how ‘wolfy’ the product of a cross is, several generations down the line. The first-generation animals will be 50:50 in their genes, but after that, the shuffling of DNA that happens as eggs and sperm are made introduces messiness – second-generation wolf-dogs could have up to 75 per cent wolf genes in their genome, or as little as 25 per cent. There’s also the possibility that some purported ‘wolf-dog hybrids’ are nothing of the sort, and are just cross-breeds of German shepherds, huskies and malamutes – which already look fairly wolf-like – to create animals which appear even more like wolves. The ‘wolfiness’ of a wolf-dog hybrid, a few generations after hybridisation, is impossible to pin down without genotyping. And even with that genetic measure of wolfiness, it’s difficult to know how this would relate to the potential behaviour of an individual animal.

There are also concerns about wolf-dog hybrids on the other side as dog genes make their way into the genomes of wild wolves. Genetic studies have shown that 25 per cent of Eurasian wolf genomes contain dog ancestry. This is problematic from a conservation perspective – could an injection of domestic dog genes into wild, grey wolves cause problems for Canis lupus? Wolf populations have declined in Europe, under pressure from both hunting and the fragmentation of habitats. But hybridisation could also supply beneficial genes and traits. North American wolves got their black coat colour by interbreeding with dogs centuries, if not millennia, ago. Most hybridisation appears to occur through free-ranging male dogs mating with female wolves, but one recent study showed up dog mitochondrial DNA in two Latvian wolf-dog hybrids. Mitochondrial DNA is exclusively inherited from the mother, so the only way that this DNA could have ended up in wolf genomes is by female dogs having mated with male wolves. Once dog genes have entered wolf populations, it’s very difficult to remove them. Some hybrids look a bit like dogs, but many look exactly like wild wolves. So experts have advised that the best way of reducing the impact of hybridisation is to reduce the number of free-ranging dogs. Once they mate with wild wolves, it’s too late.

Hybridisation raises all sorts of questions. There are biological questions about the integrity of species, and about just how much interbreeding occurs across our once sacrosanct species boundaries. If there’s plenty of interbreeding, with fertile offspring, does this mean our species boundaries are too narrow? These are widely debated questions right now. But in fact, taxonomists, the people who make it their business to name and circumscribe species, have never been quite as rigid as textbooks may have led us to believe. Species are simply snapshots of evolutionary lineages – diverging (and sometimes converging). They are defined by being diagnosably different from the nearest cousins on the tree of life. But sometimes they are defined for human convenience – especially when it comes to conferring separate species names on domesticates and their wild ancestors.
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The potential for hybridisation also leads to ethical questions about the ‘contamination’ of wild species with genes from domesticated species. Having created domesticated species, we’re now keen to preserve any surviving, closely related wild ones. But does this invoke an idea of the purity of species that just doesn’t really exist in the real world? That’s a challenging question, and one that will only become more pressing as our own population grows, and the species we’ve become allied with burgeon alongside us. It’s such a conundrum. The species that have become our allies have secured their future, by becoming companionable, useful, even indispensable to us. But together, we represent a threat to whatever wildness remains.

It seems that the safest way for humans and wolves to co-exist on the planet is to avoid each other. Our ancestors once tolerated wild wolves – long enough to domesticate them. Wolves may be naturally much more shy around humans now than they were in the past. Wolves were changed by becoming domesticated dogs, in so many ways, but the wild wolves may have changed as well. Persecution and hunting of wild wolves probably exerted a selection pressure of its own – the most successful wolves are likely to have been the ones that stayed away from humans. Wolves that are more fearful, and that avoid us, may be products of human-mediated selection – as much as dogs are.

The genetics of grey wolves and dogs suggests that the wolf lineage which gave rise to dogs is now extinct. Times were tough around the last glacial maximum, so that’s certainly possible. But there’s another way of looking at the family tree – that particular lineage of wolves is not extinct at all; in fact, it’s the most populous branch of the wolf family tree: dogs. Genetically speaking, dogs are grey wolves. Most researchers simply subsume them within the grey wolf species, Canis lupus – not a separate species, the previously recognised Canis familiaris, but a subspecies: Canis lupus familiaris.


So that terrier, that spaniel, that retriever that you know so well … it’s a wolf at heart. But a much friendlier one – even more tail-wagging, hand-licking, and altogether less dangerous – than its wild cousins.