Platypus Facts: A Fascinating Mammal That May Be in Trouble

A wild platypus in Tasmania
Photo by Klaus, CC BY-SA 2.0 license

The platypus (Ornithorhynchus anatinus) is a strange and interesting animal. It’s a mammal and is covered by fur, but it has a large structure resembling a flattened bill at the front of its head. It also lays eggs. The animal lives in Australia. Unfortunately, researchers at the University of New South Wales say that its population is in trouble.

Three groups of mammals exist: placental mammals, marsupials, and monotremes. Humans and many other animals are placental mammals. The baby develops in the uterus. It’s attached to the placenta via the umbilical cord. The placenta is in turn attached to the lining of the uterus. Animals such as kangaroos and wallabies are marsupials. The baby is delivered in a very immature state. It then climbs into its mother’s pouch, where it attaches to a nipple and completes its development. Platypuses and echidnas are monotremes. They lay eggs in which the youngsters develop. This seemingly primitive feature doesn’t mean that they are simple animals, however.

When the preserved body of a platypus (or a duck-billed platypus) was first observed by European scientists, they thought that the animal was a fake. They believed that the its body had been created by sewing parts of different animals together. 

In addition to its unusual bill, the platypus has a wide and flat tail, webbed front feet, and partially webbed hind feet. The hind feet act like a rudder and a brake when the platypus swims. The animal’s fur is brown, thick, and waterproof. A patch of white fur is located under each eye. Grooves behind the bill lead to the ears. 

The male has a spur on each ankle that leads to a venom gland. The gland is an unusual item for a mammal. The venom may be used when males are competing for a mate. It’s also applied when the male feels that he’s in danger. It’s said to be very painful for humans but not dangerous. 

A platypus in Queensland
Photo by Stefan Heinrich, CC BY-SA 2.0 license

The platypus is found in the eastern part of Australia and in Tasmania. It’s most often active at dawn or dusk or during the night. It’s sometimes seen during the day, however. The animal is found by streams and rivers in lowland areas and all the way up to alpine level. It’s a solitary animal. It feeds on aquatic invertebrates that it digs out of the stream or river bed with its bill or catches in the water. Researchers have discovered that the bill has several features to help the animal catch its food. It’s sensitive to pressure and to the weak electric currents produced by the muscles of prey animals. The platypus sleeps in a burrow near the water. It’s a great swimmer, but it’s not so good at walking on land.

After mating and a gestation period of twenty-one to twenty-eight days, the female lays eggs in her burrow. Two eggs are generally produced. They have a leathery covering and are incubated for about ten days. The female curls her body around the the eggs to keep them warm. She periodically leaves the burrow in order to feed.

Once the eggs hatch, the youngsters nurse for around three to four months. The female has mammary glands, but the glands don’t have nipples. The milk is released from pores instead. After the nursing period ends, the youngsters emerge from the burrow. Shortly before they do this, they lose their teeth. From then on they use hardened gum tissue in place of teeth. A platypus lives for around twenty years.

The IUCN (International Union for Conservation of Nature) has established a Red List in which it classifies organisms according to their nearness to extinction. At the moment, the platypus is classified in the Near Threatened category. The status is based on a 2014 population assessment. Some older sources of information still classify the animal as common, but others say that the animal’s distribution hasn’t been sufficiently studied in order to make an accurate assessment of its status.

Researchers at the University of New South Wales have a more alarming view of the platypus's situation. They’ve recently published a paper describing potential problems for the animal. They believe that we need to act now to prevent it from disappearing. The researchers say if we don’t take any steps to help the platypus, it’s headed for extinction.

One threat to the animal’s existence is habitat disruption. This disruption has arisen due to factors such as land clearing for agriculture and alteration to water resources by dam creation. Dams have caused rivers where the platypus lives to dry up. Climate change and drought are also affecting the animal’s life.

Understandably, the alarming report has attracted attention. It has only recently been released, however. I think we should definitely pay attention to the concerns that have been raised. It would be interesting to discover the opinions of scientists in other areas and institutions, though. If the somewhat dire predictions of the UNSW scientists are supported by other researchers, we need to take action now in order to protect the animal.

References

• Platypus information from the Australian Museum (Although this article is useful, its information about the population status of the platypus is out of date. The latest information is in the IUCN Red List resource below.)

• More information about the platypus from the Encyclopedia Britannica

• Status of the platypus (based on a 2014 population assessment) from the IUCN

• The platypus is in trouble from the University of New South Wales

Nutritious Pumpkins and a Waste Problem at Halloween

Pumpkins are an enjoyable part of fall.
Image by pixel2013, public domain license

Carving a pumpkin is an essential component of Halloween for many people. Huge containers of the fruits are currently being unloaded in my local supermarkets or placed in a strategic place for customers to explore. Visiting a pumpkin patch to choose the perfect fruit is a fun event for children. A problem arises after Halloween, though. What do we do with all the pumpkins? For many people, the answer is to throw them in the garbage. This is a waste of food because they are nutritious fruits. It’s also bad for the planet when pumpkins collect in a landfill. They don’t decompose properly in this location and they produce methane. Methane is a greenhouse gas that contributes to climate change. 

Pumpkins contain important nutrients. The fruit is a superb source of beta-carotene, which our body converts into vitamin A. Beta-carotene and other carotenoids give pumpkin flesh its rich orange colour. The fruit is also a good source of vitamin C, riboflavin (or vitamin B2), vitamin E, potassium, copper, manganese, and dietary fibre. It contains smaller but still beneficial levels of many other nutrients. It’s very low in fat. Like all foods from plants, it contains no cholesterol.

I sometimes use canned pumpkin as a replacement for fat in recipes. It works well and adds extra nutrients, though the levels of some of them are reduced by the heat of cooking. I also eat the canned fruit throughout the year as dessert. I like to buy unsweetened pumpkin puree and then if I choose to sweeten it use a method that I prefer. Pumpkin seeds are another tasty and nutritious treat. They are a great source of protein, magnesium, zinc, and other minerals. 

Halloween lanterns
Image by rescueram3, public domain license

Several varieties of squash are known as pumpkins. Most belong to the Cucurbita pepo species. The different cultivars of the species can look like vastly different vegetables. The ones grown for Halloween jack-o'-lanterns may not be the tastiest type. Buying a sweeter and tastier kind means that the flesh can be eaten while the rind is used for decoration. It's a shame that a nutritious fruit is discarded, but it would be an even greater shame if its disposal harmed the environment. Composting the rind and any unwanted flesh after Halloween would be better for the environment than throwing the fruit in the garbage. It’s recommended that the pumpkin is smashed before it’s composted at home.

In Metro Vancouver, where I live, food and yard waste can be placed in green bins provided by the city and are collected weekly for composting. My city’s recycling depot sells home composters for a reasonable price. Metro Vancouver Solid Waste Services says that more than thirty percent of the material sent to local landfills is compostable. They also say that the green bin system in the area is helping the problem, however.

Some communities hold pumpkin-smashing events after Halloween. I've never attended one, but they sound like fun. The remains of the fruit are often taken to a local compositing facility after the event. Sometimes people smash the pumpkins, but in one event in British Columbia the pumpkins are dropped from the top of fire ladders. Entertainment followed by composting sounds like a great combination.

Large pumpkins
Image by Capri23auto, public domain license

If a family has access to similar services or events to the ones described above or if Halloween pumpkins are accepted for composting in a nearby location, I think it’s important to take advantage of the situation (if this is possible). It’s hard to confirm some of the statistics that news sites publish, but there seems to be widespread agreement that many pumpkins are wasted at Halloween and end up in the garbage. The world’s pumpkins are probably not as serious a contributor to climate change as many other factors, but every effort to help the environment can be valuable.

References

• Nutrients in pumpkins from Self Nutrition Data
• Nutrients in pumpkin seeds (roasted and without salt) from Self Nutrition Data
• How to keep your Halloween pumpkins out of landfills from the CBC (Canadian Broadcasting Corporation)
• Pumpkins are wasted at Halloween from Science Alert

A Strange Nematode in Mono Lake That Has Three Genders

A new species of nematode has recently been discovered in California’s Mono Lake. According to researchers at the California Institute of Technology, the worm has three genders. In addition, it can survive an arsenic level that is 500 times greater than the level that kills humans and it carries its young inside its body. It sounds like a fascinating creature.

Members of the phylum Nematoda are also known as roundworms. Though they are often referred to as “worms”, they aren’t closely related to earthworms. They do have a slender and elongated shape, however. They are common animals. The group contains both parasites and free-living species that live in a wide variety of environments. They range from microscopic in size to several feet in length. The photo below shows a different species of nematode from the ones discovered in Mono Lake, but it gives the general idea of a roundworm's appearance.

A scanning electron micrograph of a soybean cyst nematode and its egg
Agricultural Research Service, public domain license

Mono Lake is located near the town of Lee Vining in Mono County, California. Like the nematodes that live there, the lake is interesting. It has a surface area of around 70 square miles and has no outlet. Its salinity is three times greater than that of sea water. Its pH of 10 makes it an alkaline or basic environment. Despite its seemingly inhospitable nature, the lake contains life. Caltech researchers have recently discovered that eight species of nematodes live in the lake, including the one described above. Before the discovery, only two animal species (a brine shrimp and a diving fly) plus algae and bacteria were known to live in the lake. The newly-discovered nematodes include predators, parasites, and ones that “graze” on microbes. 

An aerial view of Mono Lake in California
Ron Reiring, CC BY 2.0 license

The researchers have been able to culture one of the eight nematode species that they discovered in the lake. They’ve placed this animal in the genus Auanema but haven’t given it a species name yet. Its resilience to arsenic may be an adaptation that enables it to survive in the lake. It’s classified as an extremophile, or one that can live under extreme conditions compared to those required by humans. Its mouth structure suggests that it’s a microbe grazer.

The species exists in three forms: female, male, and hermaphrodite. A hermaphrodite contains both female and male reproductive organs. The eggs hatch inside the roundworm that bears them, who gives birth to live young. A relative of the species in Mono Lake (Auanema rhodensis) also exists in three forms. In this species, the females produce eggs, the males produce sperm, and the hermaphrodites can produce eggs and sperm. The identity of the chromosomes in the gametes, and the possible genders of the offspring in each parental combination appear to be unusual, however. The species was first discovered in 2018 and is still being studied. The studies might apply to the species found in Mono Lake, though this isn’t necessarily true.

Learning about the living creatures in the lake is a very interesting endeavor and could also be useful, for multiple reasons. Understanding how the animals survive in their seemingly harsh environment could be important with respect to organisms that have benefits for humans. Understanding the details of the worm's reproductive system could also be important, even with respect to human biology. 

It’s not outside the realm of possibility that understanding chromosome behaviour in nematodes could explain some situations in humans. The species has X and Y sex chromosomes, as humans do. In general, the cells of female humans have two X chromosomes and the cells of males have an X and a Y chromosome. Some of us have a slightly different chromosome collection, however. The variations in Auanema may help us to understand this situation and perhaps even lead to benefits in humans. Even if this isn't the case, the new species of Auanema sounds like an intriguing animal that is worth studying.

References

• Otherworldly worms detected in Mono Lake from the Science Daily news service
• Some facts about nematodes from the Encyclopaedia Britannica
• Information about Auanema rhodensis from the phys.org news service
• Mono Lake facts from Carleton College

The Indian or Malabar Giant Squirrel: Multicoloured and Beautiful

The Indian or Malabar giant squirrel (Ratufa indica) is a beautiful animal. It has the general body form of the squirrels that live in North America, but its thick and often multicoloured coat gives it a distinctive and very attractive appearance. The species is found only in India.

An Indian or Malabar giant squirrel in Kerala
Photo by Amara Bharathy, CC BY-SA 4.0 License

The genus Ratufa contains four species. All of them are found in South and Southeast Asia. They include: 

• Ratufa affinis (the cream-coloured giant squirrel, which is a mixture of a darker colour and cream)
• Ratufa bicolor (the black or Malayan giant squirrel)
• Ratufa indica (the Indian or Malabar giant squirrel)
• Ratufa macroura (the grizzled giant squirrel)

The Indian giant squirrel’s coat is an interesting mixture of black, brown, beige, dark red, and maroon. The pattern varies. The black fur sometimes has a purplish or even slightly blue tinge. The cheeks, chest, and belly of the animal are generally white or cream, but the belly is sometimes orange. The squirrel’s ears are short and rounded and have tufts of hair at the top. The tail is very long. In the photos that I've seen, the animal always seems to be wide eyed. These features give the squirrel an appealing appearance.

The head and body of the adult ranges from ten to eighteen inches long. The tail is at least as long as the head and body and is usually longer. In some animals, the tail reaches a length of two feet. The animal weighs around four pounds.

At the time when I wrote this post, the Indian giant squirrel was in the news because of some interesting photos of the animal that had been published on the Internet. In some photographs, the squirrels had distinctly blue patches of fur and were described as having a “rainbow” coat. It would be interesting to know how accurate the colour rendition was in the photos.

I found one person’s photograph published on two sites. The squirrel’s fur looked purple on one site and bright blue on the other, which makes me a bit suspicious. I know that some cameras have problems with depicting certain colours accurately, but since the photograph was the same one in this case and the images were viewed on the same computer monitor, that doesn’t seem to be reason for the different colours. 

Some Indian giant squirrels do appear to have navy blue areas on their coat, but I’d like to know how bright the blue can get. Even without blue fur, the squirrels are attractive animals, though. The multiple colours in their coat may help to camouflage them as they move through the tree canopy. I’d love to see the animals in person. 

Another Indian giant squirrel
Photo by Yathin S. Krishnappa, CC BY-SA 3.0 License

The Indian giant squirrel is diurnal (active during the day) but is most often seen in the early or late hours of the day. It lives in deciduous or evergreen forests in the upper canopy of the trees. It’s able to jump from one tree to another and rarely comes to the ground. The animal builds multiple nests of twigs and leaves. The nests are used for sleeping and for rearing the young. 

The squirrel is a solitary animal, except when the female is rearing her offspring. It’s omnivorous and feeds on fruits, nuts, flowers and leaves (at least occasionally), insects, and birds’ eggs. It also chews bark at times. It's able to manipulate food with its front paws. Like many fruit eaters, the animal plays an important role in its environment by spreading plant seeds to new areas in its feces. Potential predators of the squirrel include birds of prey, leopards, and perhaps certain snakes. The squirrel is said to be quite shy when humans are near.

The gestation period may be four to five weeks and one or two offspring may be produced per mating. Much more research needs to be done in this area. There appear to be quite a few gaps in our knowledge of the animal. According to the IUCN (International Union for Conservation of Nature), the lifespan of the squirrels is about twelve years. An animal in captivity apparently lived for twenty years, however.

The IUCN last assessed the animal’s population in 2016 and classifies the population as “Least Concern” in its Red List, though it didn’t state the size of the population. It also says that the population is decreasing, however. The Red List classifies animals according to their nearness to extinction.

It’s surprising how hard it is to find published information about such a common and attractive animal as the Indian giant squirrel. I hope that more research is done and that it becomes readily available outside of India.

References 

Indian giant squirrel entry at the IUCN

Facts about the squirrel from a zoologist at the Uttaranchal (P.G.) College of Bio-Medical Sciences & Hospital

Ratufa indica information from animaldiversity.org, University of Michigan

Interesting Facts About the Endangered Red-Crowned Crane

The red-crowned crane (Grus japonensis) is an attractive bird from East Asia. It's a large animal that has some interesting behaviors. The bird gets its name from the color of a patch of bare skin on the top of its head. The patch is red and becomes brighter during the mating season. The difference in the color intensity shows up well in the two photos in this post. Sadly, the crane is endangered, mainly due to activities by humans.

A red-crowned crane in Kushiro Shitsugan National Park, Japan
Photo by Tzuhsun Hsu, CC BY-SA 2.0 License

Distribution

A resident population of red-crowned cranes is found on the island of Hokkaido in Japan, where the Kushiro Shitsugan National Park is located. The crane population is increasing here. Migratory populations of the bird are seen in China, Russia, and the Korean Peninsula. Unfortunately, these populations are in trouble.

Physical Appearance

The red-crowned crane has a white, black, and red coloration. Its face and its long neck are black, except for a white patch on the side of the face and the top of the neck. The colors make a nice contrast with the red crown. Most of the body is white, but there are black patches on the wings. The bird has a long bill and long and thin legs, like other cranes.

Adult red-crowned cranes are around five feet tall and have a wingspan of around eight feet. They weigh up to twenty-five pounds and are one of the biggest cranes on the planet. The birds are impressive animals.

Red-crowned cranes displaying
Photo by cyberfox, CC BY 2.1 JP license

Daily Life

The crane lives in a large flock. It forages on wetlands with the other birds in its flock. These wetlands include both freshwater and saltwater marshes and the land beside rivers. The bird also enters the rivers to feed. It has an omnivorous diet and eats fish, amphibians, aquatic invertebrates, and small mammals as well as grass, reeds, and berries. It also eats grain distributed by humans.

In Japan, people support the crane population by feeding the birds grain and fish at feeding stations and other areas. At least some of the people of Hokkaido respect the birds and have done much to help them. The birds face snow and ice in winter on the island, but this doesn't seem to bother them. They are said to roost in deep water that doesn't freeze.

The birds have an interesting display in which they gather in groups, throw their head back, and call, as shown in the photo above and video below. They may also expand their wings and jump into the air during the display. The display is often referred to as a dance. It takes place at any time of the year but seems to be most common during the breeding season.

An Important Symbol

The birds reportedly live for up to twenty years in the wild and up to forty years—or even longer—in captivity. The animal's lifespan hasn't been well studied. The birds have become a symbol of loyalty, long life, and luck. They are used as an icon on many products and services in Japan. A stylized bird is the symbol for Japan Airlines. When they are referred to symbolically, the birds are often called tancho cranes.

Reproduction

Red-crowned cranes are monogamous, which means they keep the same partner for life. They build their nest in wetlands containing areas of deep water. The females most often lay two eggs. Both the female and the male incubate the eggs. Incubation lasts for around thirty days. The youngsters stay with their parents until the next breeding season.

Why Are Red-Crowned Cranes Endangered?

The birds are in trouble for multiple reasons. The loss of their wetland habitat is the main one. Humans are taking over the cranes' traditional habitats for agriculture and industry. Pollution, the presence of invasive species, and a changing environment are other threats. The bird sometimes collides with power lines during flight.

The IUCN (International Union for Conservation of Nature) classifies the crane as endangered. Only around 1,830 mature individuals are believed to exist. The IUCN says that the overall population is decreasing.

Some people are helping the cranes. The birds are doing quite well on the island of Hokkaido because of these efforts. The migratory populations need help, however. I hope they get it. The red-crowned crane is a beautiful and intriguing bird.

References

Information about the red-crowned crane from Smithsonian's National Zoo & Conservation Biology Institute

Grus japonensis entry on the IUCN Red List

Facts about the bird from the International Crane Foundation

The Greater Ani: A Cuckoo and Its Egg-Laying Behaviour

The greater ani (Crotophaga major) is a Central and South American bird in the cuckoo family, or the Cuculidae. It's a relatively large cuckoo with plumage that is an attractive blue-black colour. It has a large protuberance on its upper bill, white to yellow irises in its eyes, and a long tail. Researchers at Princeton University have recently made some interesting discoveries about the bird's egg-laying behaviour. The behaviour is atypical for its family, although the bird sometimes behaves more like a typical cuckoo. Cuckoos are generally social parasites that lay their eggs in other birds' nests.

A greater ani; photo by Arthur Chapman, CC BY 2.0 license

Daily Life of the Bird

Greater anis live in tropical lowland forests next to water. Cornell University says that not much was known about the birds until recently. A boat is often needed to find them and they fly quickly to another location when disturbed. Research is gradually revealing details about their lives, although some need to be confirmed and more need to be discovered.

The birds are very social. They live in flocks that maintain a territory. They feed in a loose group and eat insects and occasionally small vertebrates, such as lizards and frogs. They occasionally feed on fruit. The birds give frequent contact calls as they forage so that individuals know where the other members of their group are located. They climb down branches that reach the water to drink.

The birds roost in large groups, except during the breeding season. They rarely come to the ground, but when they do, they move by walking or hopping. They sometimes enter the water and are strong swimmers. They seem to like sunbathing and sometimes raise their wings as they perch on a sunny day. They also raise their wings after rain, presumably to dry them. The birds preen frequently.

Greater anis are said to have an unpleasant smell, especially when they are in a group. When they are close together, the birds often call at the same time. Christina Riehl a behavioral ecologist at Princeton University, says that the group call "sounds like an outboard motor or an eggbeater."

Another greater ani; photo by Dominic Sherony, CC BY-SA 2.0 license

Reproduction

Unlike typical cuckoos, greater anis usually gather in groups of two or three pairs to build a communal nest. All of the females in the group lay their eggs in this nest and each bird guards all the eggs instead of just their own. The nest is made of leaves and twigs and the eggs are piled on top of each other, as a photo in the last reference below shows. As some reports say, the birds seem to be putting all of their eggs in one basket. The eggs are covered by a calcium carbonate layer and are white at first. As this layer is gradually removed by activities in the nest, a blue layer is revealed.

According to the Cornell Lab of Ornithology, "all of the individuals in the group" build the nest, protect the eggs, incubate them, and feed the hatched youngsters. While this might seem like an ideal society, researchers have discovered that a female sometimes throws an egg laid by another bird in the group out of the nest before she has laid her own egg. Once she has laid her first egg, however, she no longer ejects others. The group dynamics need to be studied further.

Scientists have also discovered that if the communal nest is destroyed by a predator such as a snake, the birds may revert to typical cuckoo behaviour. The females may produce more eggs and deposit them in the nests of other greater anis (but not in the nests of other species). Here the eggs will hopefully be protected and eventually hatch. Some females simply wait until the next year to breed again, however. Incubation seems to last for somewhere between eleven and fourteen days.

Researchers have studied the breeding success of the birds that become parasitic and the ones that rear their young in a communal nest. They've found that while the birds that become parasites lay more eggs in a year, the parasites and the communal mothers produce about the same number of offspring.

Discovering More About Greater Anis

Hopefully researchers will discover more about greater anis and their lives in the near future. Some sites reference information about the birds that was discovered in the 1940s. This information isn't necessarily wrong. With the newer research equipment and techniques that exist today, however, it should be possible to obtain more accurate or more detailed facts about the species.  I would like to know more about the community activity at the nesting site and to discover or confirm information about the relative roles of the males and the females. It will be interesting to see what scientists discover next.

References

Crotophaga major facts from the Cornell Lab of Ornithology
Information about the greater ani from BirdLife International
Put eggs all in one basket or spread them around? from the ScienceDaily news service
A parasitic cuckoo from Science News

The Groundcherry and CRISPR Manipulation of Genes

The groundcherry (Physalis pruinosa) is an interesting plant with a flavourful fruit and potential benefits for humans. Unfortunately, it has problems as an agricultural crop. It isn't easy to grow and the fruit tends to drop to the ground before it's ripe. This tendency and the small size of the fruit gave the plant its common name. A team of U.S. researchers has successfully altered some of the features of the plant with a method of gene editing known as CRISPR. This could be helpful in creating a new food crop for humans.



Photo credit: Physalis pruinosa by Carstor, CC BY-SA 3.0 license

The Groundcherry Plant

I've never tasted a groundcherry, but it sounds like an intriguing fruit. The flavour is said to be both sweet and sour and to contain elements of pineapple, vanilla, and tomato. It's not as sweet as some popular fruits, however. The smell of the fruit is said to be "intoxicating."

The groundcherry plant belongs to the family Solanaceae, which is commonly known as the nightshade family. Tomatoes also belong to this family. Some other members of the genus Physalis are known as groundcherries as well, so when reading about the fruit it's important to check the species that is being discussed. The members of the genus are known for the papery husk or capsule that partially or completely surrounds the fruit. The capsule is derived from the calyx of the flower. A popular ornamental plant in the genus (Physalis alkekengi) is known as the Chinese lantern plant. Its orange capsules are attractive and much admired.



Photo credit: Chinese lantern plant by Shu Suehiro, CC BY 3.0 license

A Basic Introduction to CRISPR

CRISPR technology arose from an observation in certain bacteria. The bacteria had developed a method to cut and destroy strands of viral DNA (deoxyribonucleic acid) that invaded the cell. The process involved a bacterial enzyme known as Cas9. A piece of bacterial RNA (ribonucleic acid) joined to a specific location on the viral DNA and then the enzyme broke up the DNA.

The bacterial system was reminiscent of own immune system because it "remembered" the virus attack. If it was infected by that type of virus again, it produced the appropriate RNA to find and bind to the correct region on the DNA so that Cas-9 could break it up.

Researchers released that they could use a similar technique to remove a section of an organism's DNA in a specific location and then insert a gene of their choice. A gene is a section of DNA that codes for a particular protein. The code is how genes control the characteristics of an organism.

Scientists create a piece of guide RNA that binds to the area of DNA that is of interest. The Cas-9 enzyme then breaks the DNA in that area. The scientists use the cell's DNA repair mechanism to insert the desired genetic material into the broken area and repair the break.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The gene-editing technique is sometimes referred to as CRISPR-Cas 9. Understandably, the process is worrying some people because it appears to be such a precise and efficient way to alter the genes of an organism. Genetic modification of any kind requires great care. It could have great benefits if done responsibly, however.

Modifying the Groundcherry Genome

By using CRISPR and their knowledge of the tomato genome, the researchers have created groundcherry plants that have a more compact form (and therefore are more manageable by growers) and that produce fruits in clusters instead of singly. In addition, they have been able to create larger and denser fruits. They haven't yet modified the taste, but that's their next goal.

Plant growers can use selective plant breeding techniques to develop desirable features in cultivated plants. Changes that make the groundcherry a better crop for humans could take a very long time, however. CRISPR is much faster and should produce new fruit to eat quite soon.

Photo credit: Flower of Physalis coztomatl by Carstor, CC BY-SA 3.0 license

Feeding Hungry People

At the moment, the groundcherry is said to be an orphan crop. An orphan crop is cultivated on a very small scale or is used for subsistence. Problems such as a low yield or quick decay once it's harvested prevent it from becoming a mainstream crop. This is a shame with respect to the groundcherry because it's said to be a nutritious fruit.

The groundcherry research could be important. A professor of nutrition at New York University is impressed by the recent research, but she points out that producing larger quantities of nutritious food is not the only requirement for feeding the world. Problems such as the existence of war and the lack of transportation to move food crops to where they are required need to be solved. Preservation of food during transport and before distribution is also a concern.

As the Earth's population grows and the need for quickly grown and nutritious plants increases in order to feed hungry people, CRISPR could become very important in improving crops, whether we like it or not. 

References

CRISPR basics from John Hopkins School of Medicine

What are genome editing and CRISPR-Cas 9? from the U.S. National Library of Medicine, National Institutes of Health (NIH)

Groundcherries: A modified fruit you may want to try from CNN

An orphan crop that could be the next strawberry from the Howard Hughes Medical Institute 

The Critically Endangered Resident Killer Whales in Puget Sound

A group of killer whales or orcas (Orcinus orca) live in and around Puget Sound in the U.S. state of Washington throughout the year. Unfortunately, these animals are critically endangered. In January, 2019, a new calf was seen. This is potentially great news, since no calf has been born and survived in the group in three years. A researcher who studies the animals tells us not to get too excited because the calves have only a fifty percent survival rate, however. The Puget Sound group last came to the public's attention in 2018 with the sad story of Tahlequah, a female who carried her dead daughter for seventeen days before she released her.

A killer whale or orca

Credit: skeeze, public domain license

Puget Sound

Puget Sound is located in the northwestern part of Washington State. It's an inlet of the Pacific Ocean and has a complex, branched structure. It's connected to the Strait of Juan de Fuca, which comes directly from the Pacific Ocean, and the Strait of Georgia, which travels into Canada. The boundary between the United States and Canada travels along the middle of the Strait of Juan de Fuca and along the middle of the southern part of the Strait of Georgia. (The northern part of the strait is located in Canada).The map below shows the connections. The water channels shown in the map are sometimes collectively referred to as the Salish Sea.

Map of Puget Sound

Pfly, CC BY-SA 3.0 License

Killer Whales in the Puget Sound Area

Four groups of killer whales are recognized in the northeastern part of the Pacific Ocean: the northern residents, the southern residents, the transients, and the offshores. According to the Encyclopedia of Puget Sound published by the University of Washington, the groups differ in morphology, behaviour, and diet.

The southern resident killer whales (SRKW) live in both the northern United States and southern Canada. They are most often seen in the Strait of Juan de Fuca, the southern part of the Strait of Georgia, and Puget Sound. The group as a whole exists in several smaller collections. The J, K, and L pods frequent the Puget Sound. These pods consist of 74 whales in total. Three of them have died in the last year.

The whales are in trouble due to the lack of sufficient Chinook salmon to eat. Multiple populations of the salmon are endangered, like the killer whale population that enters Puget Sound. The reason why the salmon and whale populations in the Salish Sea are in trouble is multifactorial. As some people have said, there are no easy answers, but if we want to save the whales we need to take action soon.

Whales Of Concern

The new calf was born to a female in pod L known as L77. It was estimated to be a few weeks old when it was discovered with its pod in the eastern part of the Strait of Juan de Fuca. Hopefully it will survive to adulthood and produce calves of its own.

Unfortunately, a young whale in the K pod known as K25 hasn't been doing very well since his mother died in 2017. One researcher says that the youngster is continuing to lose weight and may not live though the upcoming summer. Young whales nurse for around a year and then rely on fish that their mother catches for them for some time afterwards. Whale J17 is also very thin and is a concern. She was Tahlequah's mother.

Though researchers are often reluctant to interfere in the lives of the animals that they are studying, it's sometimes hard to avoid doing so, especially when a population is endangered. J50 (or Scarlet) was a young whale in a very emaciated state. A veterinarian from the Vancouver Aquarium injected her with antibiotics to fight infection by firing a dart at her. Canadian and American officials were creating a plan to capture and treat her if she fell behind her pod. Before the rescue plan could be put into operation, Scarlet was pronounced dead in September, 2018. Though her body was never found, her family was seen without her three times. She hasn't been seen since.

Tahlequah the Killer Whale

The story of Tahlequah (J35) and her calf captured the public's imagination in 2018, and understandably so. Her calf died a few hours after birth. Whale calves are born underwater, but their mother quickly pushes them to the surface so that they can breathe. If a calf dies, it's normally dropped and sinks. Tahlequah didn't drop her calf for seventeen days and until she had swum 1,000 miles, however. She continued to hold the calf at the water's surface and carried her on her forehead as she swam, even though this interfered with her swimming and her feeding. Researchers were worried about Tahlequah's health.

Many people describe Tahlequah's behaviour as a "tour of grief." Others say that we shouldn't ascribe human emotions to other animals because we don't know what they are feeling or experiencing. It's known that whales have complex brains and behaviour, however. Tahlequah certainly behaved as though she was in mourning.

It would be a great shame if the Puget Sound whales disappeared. They are intelligent and interesting animals. It's true that other groups of the whales exist and that the population of orcas as a whole may not be in trouble. The IUCN (International Union for Conservation of Nature) classifies the total population of the animal in its Data Deficient category, however. More research is needed to determine its true status. I think that the unique characteristics of each group of whales are important. I hope the orcas in the Salish Sea survive.

References

New orca calf seen in Puget Sound from the phys.org news site

Killer whales in Puget Sound from the Encyclopedia of Puget Sound, University of Washington

Tour of grief is over for killer whale from CNN

Attempts to help whale J50 from NPR

United to save salmon and orcas from The Seattle Times

George the Hawaiian Tree Snail and Why His Death Matters

George the Hawaiian tree snail died on New Year's Day, 2019. He was the last of his species known to exist, which means that the species (Achatinella apexfulva) is very likely extinct. George was born in a captive breeding facility and spent his entire life there as scientists tried to save him and his companions. He was named after Lonesome George, a Pinta Island tortoise who was the last of his kind. Lonesome George died in 2012 and was believed to be just over a hundred years old. Many more of the world's land snails are in trouble besides the ones in Hawaii. It's a worrying situation.

Tree snail shells collected circa 1933 and displayed at the Bernice Pauahi Bishop Museum

Credit: Hiart, public domain license

Some Facts About Land Snails

• Snails belong to the phylum Mollusca and the class Gastropoda. 
• Land snails such as O'ahu tree snails (their official name) have a coiled shell. They are able to retract into the shell for protection. 
• The animals breathe by means of a single lung. 
• Gases enter and leave the lung via an opening called a pneumostome, which is located on the right side of the body. 
• The snails have a specialized tongue called a radula. The radula contains rows of tooth-like structures that enable it to act as a rasp. 
• A snail moves by means of a muscular foot travelling over a layer of mucus that it deposits on the ground.

O'ahu Tree Snails

O'ahu tree snails belong to the genus Achatinella and are endemic to Hawaii. According to a Government of Hawaii document published in 2005, 41 species may have existed at that time. The document says that all of the species in the genus were endangered and about half of them were believed to be extinct. The exact number that exists today is uncertain, but it's almost certainly much less than 41. This is a sad comment about a type of snail that was once abundant in Hawaii. Hundreds of species existed at one time.

Some species of tree snails survive today, some that were thought to be extinct have been rediscovered, and some new species have been discovered. Nevertheless, the group as a whole is in trouble. Researchers say that wild populations need to be protected and that if this can't be done members of the species need to be brought into captivity to enable them to survive.

As their name implies, O'ahu tree snails live in trees, though they may also be found in shrubs. They have striped shells and are often attractive. Most species are thought to be nocturnal. They feed on the fungi, algae, and other organisms that grow on leaves but don't eat the leaves themselves. They can live into their teenage years and don't reproduce until they are three to five years old. They give birth to relatively few offspring (less than ten) per year. The youngsters are born live. Only one is produced at a time.

Based on their occurrence in Native Hawaiian stories and their use in leis, O'ahu tree snails must have been very abundant when Polynesians arrived in Hawai'i. Quote from The Government of Hawaii O'ahu tree snail fact sheet

Achatinella apexfulva from 1850

Credit: Naturalis Biodiversity Center and Wikimedia Commons, public domain license

Why Are the Animals in Trouble?

Researchers believe that several factors are responsible for the decline in tree snails. These include loss of natural habitat, the introduction of rats, and the introduction of the rosy wolfsnail, or Euglandina rosea, in 1955. This snail is a carnivore and a predator. It was introduced in the hope that it would eat the giant African land snail, a huge snail that feeds on agricultural crops and is a major pest. The rosy wolfsnail does eat giant African land snails, but it eats lots of tree snails as well.

National Geographic recounts a sad tale that demonstrates the swiftness of the disappearance of one species of Achatinella. The last population of Achatinella lila was counted three years ago. Around 300 snails in the species were living on a particular ridge. In April of last year, no animals could be found and the species was classified as extinct in the wild.

A Snail Named George

George was born at a University of Hawaii captive breeding facility. Not long after his birth, the other captive snails of his species—including adults and youngsters—died for an unknown reason. The researchers tried to find a mate for George but were unsuccessful. He died at the age of fourteen.

Technically, gender doesn't apply to the snails because they are hermaphrodites (animals having both male and female reproductive organs). The presence of another snail is required in order for reproduction to occur, however. The researchers chose to call George a "he." He was only around an an inch long, but he was an important animal.

Some people may wonder why the loss of a snail species is significant. A biologist who was once involved with the captive breeding of tree snails explains why in the quote below. Nature is poorer for the loss of one of its abundant components.

Anything that is abundant in the forest is an integral part of it. Quote from Michael Hadfield, biologist 

A species has a unique set of genes that may be very useful in its environment and enable the species to play an important role there. From a selfish point of view, it may also be useful to humans. The study of genes and gene combinations found in other animals can sometimes show researchers features that might help our lives.

Genetic material was obtained from George's foot. It might be possible to one day produce his species again by a cloning process, which offers a glimmer of hope. The breeding facility has other species of O'ahu tree snails besides George's, and some are doing quite well. It might be possible to increase the population of at least some species in the genus significantly. The animals may have to stay in a breeding facility or be released into an enclosed area protected from rats and predatory snails, however. Perhaps the future situation will be better than the present one.

References

O'ahu tree snail facts from the Government of Hawaii

George the tree snail dies from National Geographic

The Christmas Berry Plant and Potential Help for an Eye Disease

The Christmas berry (Ardisia crenata) is an attractive shrub in the primrose family, or the Primulaceae. It grows in the wild and as a cultivated plant. Scientists have discovered that in lab equipment a specific chemical from the plant destroys a particular kind of human cancer cell. This doesn't necessarily mean that the chemical can be used to treat cancer in humans, but the discovery is certainly interesting and may eventually have practical benefits.

The Christmas Berry plant

Credit: Dick Culbert, CC BY-2.0 License

The Christmas or Coral Berry Plant

Ardisia crenata is also known as the coral berry plant. The plant produces white to pale pink flowers in the summer and then attractive red berries at Christmas and beyond. The shrub has thick, leathery leaves that have a glossy green appearance. They are roughly oval in shape and have a pointed tip and scalloped edges. I think it's understandable why the plant is liked. The shrub generally reaches a height of one-and-a-half to three feet but is capable of reaching six feet. It reproduces by seeds and by vegetative cuttings.

The Christmas berry is native to East and Southeast Asia. It requires some shade and in nature grows as an understory plant in the forest. In the right environment, the plant grows well outdoors in
North America—sometimes too well. It's considered to be an invasive plant in certain areas, so it's often best to keep it indoors. Other plants besides Ardisia crenata are sometimes referred to a "Christmas berries". It's important that anyone interested in obtaining a plant looks at its scientific name to check whether it's really the species that they want.

Credit: Bruce Blaus, CC BY-3.0 License

The Uvea of the Eye

The new discovery is related to the uvea of the eye. The human eyeball is composed of three layers: the outer sclera, which is visible at the front of the eyeball as the white of the eye, a middle layer, and the inner retina. The middle layer as a whole is known as the uvea. It consists of the iris at the front of the eye, the ciliary body, and the choroid, which contains blood vessels.

In the illustration above, the ciliary body is shown but not labelled. It's the pink projection above and below the lens. There's only one ciliary body in an eye. It's a circular structure, which is why it looks as though there are two ciliary bodies in the eye section shown in the illustration. The structure contains the ciliary muscle, which changes the shape of the lens. It also secretes a fluid called aqueous humour. This fluid has important functions in the front part of the eyeball.

Uveal Melanoma Research

In uveal melanoma, the cells that become cancerous are the melanocytes. The function of the cells is to make a pigment called melanin. Some treatments for uveal melanoma are available. Unfortunately the cancer sometimes spreads to the liver, which can make it harder to treat. An improved treatment would be a wonderful advance.

The recent research related to uveal melanoma is exciting and hopeful, but it's important to remember that the results were obtained in lab equipment and not in living organisms. The researchers were associated with the Sidney Kimmel Cancer Center and the Ichan School of Medicine at Mt. Sinai in the United States.

The scientists investigated the effect of a Christmas berry chemical on uveal melanoma cells. The experimental compound was obtained from the plant's leaves and has the rather unappealing name of FR900359. Thankfully, the name is often abbreviated as FR. It was actually discovered thirty years ago. 

The researchers found that the chemical blocks a particular type of G protein located on the surface of cancerous uveal cells. The protein normally acts as a signaling molecule. In uveal melanoma, the protein molecule is mutated (altered), triggering a process that causes cells to become cancerous. When moderate doses of FR blocked the mutated proteins in the lab experiment, the uveal cells "appeared to revert from cancerous cells to typical uveal cells". Higher doses of FR killed the cancerous cells.

Future Research

The researchers plan to test the chemical on lab animals. If this effort is successful and the chemical is shown to be safe, they plan to test it on humans. The leader of the research team says that he's "very optimistic". Time will tell whether his optimism is justified. I very much hope that it is.

References

Ardisia crenata information from the Invasive Species Compendium (ISC)

A Christmas berry plant compound and uveal melanoma from the EurekAlert news service

Newly-Discovered Soil Bacterium May Fight Dangerous Microbes

Antibiotic resistance in bacteria is a serious problem at the moment. As microbes become resistant to the effects of the antibiotics that once killed them, some dangerous organisms are becoming much more difficult to destroy. If this process continues, there could be major and even tragic consequences for our health. Researchers have discovered a few new species or strains of bacteria in soil that offer some hope in the form of the chemicals that they produce. A multinational team at Swansea University in Wales has found a new species of bacterium in Irish soil that destroys some potentially very harmful bacteria in lab equipment.

Streptomyces sp.

Photo credit: CDC Public Health Image Library, public domain license

Special Soil

The Irish soil sample was obtained from an area known as the Boho Highlands, which is located in Fermanagh in Northern Ireland. The region contains alkaline soil. It's interesting that the soil has a reputation for healing abilities. In the past, people used to wrap some of the earth in cloth and apply the bundle to injured areas. The area was once inhabited by druids. It's important to note that harmful as well as helpful organisms live in soil, so applying soil to injuries could be dangerous. Certain components of the soil might be helpful, however.

In general, scientists have paid little attention to folk medicine, relying on experimental discoveries in the lab instead. Some scientists are now exploring materials and substances  traditionally believed to have medicinal benefits by different cultures, a subject known as ethnopharmacology. One of the scientists involved in the Boho Highlands research once lived in the area and was aware of the soil's reputation. Exploring unusual sources of help (according to current medical beliefs) seems like a good idea in our fight against harmful bacteria.

A New Version of Streptomyces

The Streptomyces genus of bacteria contains many species, some of which have proved to be very valuable for us. A large number of antibiotics have come from various members of the genus. One of the earliest was streptomycin. The bacteria exist as filaments and produce chains of spores, as shown in the photo above. Though their morphology may remind people of fungi, they are true bacteria. They are chiefly found in the soil and amongst decaying plants. They are known for the "earthy" odour that they produce. The smell is caused by a chemical called geosmin that is released when the bacteria die. 

The researchers who examined the Irish soil were looking for a new species or strain of Streptomyces, and they found one. The researchers have named the organism Streptomyces sp. myrophorea. They say that its closest known relative has “57% of genome relatedness.” The species name is not written in italics because at the moment it hasn’t been officially recognized as a new species. The bacterium releases a pleasant scent resembling that of oil of wintergreen. Its species name comes from the Greek myro, which means fragrance, and phorea, which means carrier.

The new bacterium inhibited the growth of four out of six major multi-drug resistant pathogens (microbes that cause disease), including:

·        vancomycin-resistant Enterococcus faecium

·        methicillin-resistant Staphylococcus aureus, or MRSA

·        Klebsiella pneumoniae

·        carbapenum-resistant Acinetobacter baumannii

The major drug-resistant pathogens are so important that a special collective name is used to refer to them. The ESKAPE pathogens are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and species of Enterobacter.

Gram Positive and Negative Bacteria

The researchers found that the newly-discovered soil bacterium inhibited both gram-positive and gram-negative bacteria. This is important because gram-negative bacteria are usually harder to kill. The scientists don’t know the identity of the bacterial chemical that is harming the pathogens. They are investigating this question, however.

Gram-positive bacteria (such as Streptomyces) are covered by a cell membrane, which is in turn covered by a cell wall. Gram-negative ones have a inner cell membrane and a cell wall, but they also have another membrane outside of the wall. Unfortunately, the structure of their cell covering protects them from many antibiotics.

Gram negative and positive bacteria were given their designation due to their different behaviours during a staining process known as the Gram stain test. Gram-positive bacteria appear pink after the process and gram-negative bacteria look violet. The different colours are due to the different nature of the layers around the cell. The staining process is named after Hans Christian Gram, who created it in 1884.

Hopeful Research

The research is interesting and hopeful. It was carried out in lab equipment, however, not in a living organism. Results inside the body are sometimes different from those in laboratory containers. Nevertheless, investigators are finding some interesting soil bacteria that are potentially useful in the fight against antibiotics. The new species of Streptomyces may be one of them.

The researchers involved in the Boho highlands research say that they have found other bacteria in the soil that make antibiotics. They hope that these may fight additional species of pathogens.

References

Bacteria in Irish soil halts growth of superbugs from the Eurekalert news service

Gram staining information from Carleton College

The Himalayan Marmot and a Genome for High-Altitude Life

The Himalayan marmot is a fascinating mammal because it often lives at high altitudes. It makes its home in the Himalayas and on the Tibetan Plateau. It apparently has no problem dealing with the very cold temperatures, low oxygen levels, and high intensity of ultraviolet light in much of its environment. In fact, it’s thought to have a large population. A new study has analyzed the animal’s genome and found genes that help it survive under the seemingly harsh conditions at high elevation, especially when it's hibernating in winter.

A Himalayan marmot in Bhutan

Christopher J. Fynn, via Wikimedia Commons, CC BY-SA 3.0 License

The Himalayan Marmot or Marmota himalayana

The Himalayan marmot has a wide range and can be found in Pakistan, India, Nepal, Bhutan, and China. Like other marmots, the animal has a stout body with short legs and a stubby tail. The back legs are longer than the front ones. Its coat is thick and is buff in colour with dark or black patches. One of the black patches is often on the nose and another is often on the forehead. A black line may travel down the face to connect the two areas.

Diet and Life

Himalayan marmots feed mainly on herbs and grasses but occasionally eat fruits and roots. They live in colonies, which vary in size, and spend their nights in burrows. They hibernate in groups. Winter burrows may be as deep as thirty metres. The depth enables the animals to survive the most severe environmental conditions. Nevertheless, they experience low temperatures and low oxygen concentrations during hibernation. The animal hibernates for the impressively-long time of more than six months—from late September to some time in April.

Gestation reportedly lasts for one month. Between two and eleven youngsters are said to be born in either late spring or early summer. This data needs to be confirmed, however. Reproduction is one aspect of the marmot’s biology that needs to be further studied.

Studying the Animal’s Genome

Some Chinese scientists have recently finished sequencing the genome of the Himalayan marmot. They’ve made some interesting discoveries with respect to genes that seem to be adapted to help the animal survive hypoxia (low oxygen) and cold temperatures.

The scientists compared genome activity in Himalayan marmots living at high altitude with the activity in animals living at a comparatively low altitude. The animals are found at elevations of around 1,900 to 5,000 metres. As part of their research, the scientists observing transcriptional changes in the animals.

Genes do their job by making proteins. Transcription is the process in which the instructions encoded in a gene in a DNA molecule are copied onto a messenger RNA (mRNA) molecule. The mRNA leaves the nucleus, where the DNA is located, and travels to a ribosome in the cell. Here the protein coded for by the DNA is made. The fact that transcriptional changes appeared in the scientists' study of the marmots meant that the activity of genes had changed.

The analysis of the marmot's genome is preliminary, but the researchers have already made some interesting discoveries. One is that the Himalayan marmot separated from the Mongolian marmot about 1.98 million years ago. Some other highlights of the research are described below.

Genome Discoveries

The scientists found that during hibernation there was an increased activity of genes involved in fatty acid breakdown and decreased activity of genes involved in fatty acid manufacture. The researchers also observed a decreased synthesis of amino acids, decreased breakdown of carbohydrates, and a decrease in activity of genes involved in the circadian rhythm. The circadian rhythm is a cycle of biological activity over an approximately twenty-four hour period.

The activity of a gene known as Slc25a14 and a pseudogene known as ψAamp was different in the high and low elevation marmots and may be involved in helping the animal survive under harsh conditions. A pseudogene is similar to a real gene in structure but doesn’t code for a protein. Researchers have discovered that some pseudogenes aren’t completely inactive and have a regulatory function. This appears to be the case for the ψAamp pseudogene.

In hibernating animals living at high elevation, Slc25a14 activity stimulates processes that help to protect the marmot from hypoxia. The pseudogene appears to decrease the activity of the Aamp gene, resulting in a decrease in angiogenesis, or new blood vessel formation. This may be beneficial during very hypoxic conditions during hibernation.

Previous research has shown that the brains of hibernating animals living at high altitude are exposed to temperatures near freezing and have decreased blood flow. This puts the animals at an increased risk for blood clots in the brain—or it would do, if their body didn’t respond appropriately. The new research has shown that the genes involved in blood clotting become less active. In addition, genes involved in regulating stem cells become more active. Stem cells are unspecialized but divide to form specialized ones. The activation of stem cells may enable brain cells damaged during hibernation to be replaced.

Clues for Further Research

As the researchers say, their discoveries should act as clues for other scientists. The researchers acknowledge that more research is needed, but the discoveries so far are very interesting. The Himalayan marmot is a common animal, but it seems that there is still a lot to learn about it.

References

Information about the Himalayan marmot from Wildscreen Arkive

Marmota himalayana entry from the IUCN Red List

Himalayan marmot genome offers clues to life at extremely high altitudes from the EurekAlert news service

Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome from iScience, Cell Press