A Medley of Potpourri: Aug 14, 2023

Monday, August 14, 2023

Cannibalism

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Cannibalism

Cannibalism is the act of consuming another individual of the same species as food. Cannibalism is a common ecological interaction in the animal kingdom and has been recorded in more than 1,500 species. Human cannibalism is well documented, both in ancient and in recent times.

The rate of cannibalism increases in nutritionally poor environments as individuals turn to members of their own species as an additional food source. Cannibalism regulates population numbers, whereby resources such as food, shelter and territory become more readily available with the decrease of potential competition. Although it may benefit the individual, it has been shown that the presence of cannibalism decreases the expected survival rate of the whole population and increases the risk of consuming a relative. Other negative effects may include the increased risk of pathogen transmission as the encounter rate of hosts increases. Cannibalism, however, does not—as once believed—occur only as a result of extreme food shortage or of artificial/unnatural conditions, but may also occur under natural conditions in a variety of species.

Cannibalism is prevalent in aquatic ecosystems, in which up to approximately 90% of the organisms engage in cannibalistic activity at some point in their life-cycle. Cannibalism is not restricted to carnivorous species: it also occurs in herbivores and in detritivores. Sexual cannibalism normally involves the consumption of the male by the female individual before, during or after copulation. Other forms of cannibalism include size-structured cannibalism and intrauterine cannibalism.

Behavioral, physiological and morphological adaptations have evolved to decrease the rate of cannibalism in individual species.

Benefits

In environments where food availability is constrained, individuals can receive extra nutrition and energy if they use members of their own species, also known as conspecifics, as an additional food source. This would, in turn, increase the survival rate of the cannibal and thus provide an evolutionary advantage in environments where food is scarce. For example, female Fletcher's frogs lay their eggs in ephemeral pools that lack food resources. Therefore, in order to survive, tadpoles within the same clutch are forced to consume each other and exploit their conspecifics as the only available source of nutrition. A study conducted on another amphibian, the wood frog, tadpoles showed that those that exhibited cannibalistic tendencies had faster growth rates and higher fitness levels than non-cannibals. An increase of size and growth would give them the added benefit of protection from potential predators such as other cannibals and give them an advantage when competing for resources.

The nutritional benefits of cannibalism may allow for the more efficient conversion of a conspecific diet into reusable resources than a fully herbaceous diet; as herbaceous diets may consist of excess elements which the animal has to expend energy to get rid of. This facilitates for faster development; however, a trade-off may occur as there may be less time to ingest these acquired resources. Studies have shown that there is a noticeable size difference between animals fed on a high conspecific diet which were smaller compared to those fed on a low conspecific diet. Hence, individual fitness could only be increased if the balance between developmental rate and size is balanced out, with studies showing that this is achieved in low conspecific diets.

Cannibalism regulates population numbers and benefits the cannibalistic individual and its kin as resources such as extra shelter, territory and food are freed, thereby increasing the fitness of the cannibal by lowering crowding effects. However, this is only the case if the cannibal recognizes its own kin as this won't hinder any future chances of perpetuating its genes in future generations. The elimination of competition can also increase mating opportunities, allowing further spread of an individual's genes.

Costs

Animals which have diets consisting of predominantly conspecific prey expose themselves to a greater risk of injury and expend more energy foraging for suitable prey as compared to non-cannibalistic species.

Predators often target younger or more vulnerable prey. However, the time necessitated by such selective predation could result in a failure to meet the predator's self-set nutritional requirements. In addition, the consumption of conspecific prey may also involve the ingestion of defense compounds and hormones, which have the capacity to impact the developmental growth of the cannibal's offspring. Hence, predators normally partake in a cannibalistic diet in conditions where alternative food sources are absent or not as readily available.

Failure to recognize kin prey is also a disadvantage, provided cannibals target and consume younger individuals. For example, a male stickleback fish may often mistake their own "eggs" for their competitor's eggs, and hence would inadvertently eliminate some of its own genes from the available gene pool. Kin recognition has been observed in tadpoles of the spadefoot toad, whereby cannibalistic tadpoles of the same clutch tended to avoid consuming and harming siblings, while eating other non-siblings.

The act of cannibalism may also facilitate trophic disease transmission within a population, though cannibalistically spread pathogens and parasites generally employ alternative modes of infection.

Diseases transmitted through cannibalism

Cannibalism can potentially reduce the prevalence of parasites in the population by decreasing the number of susceptible hosts and indirectly killing the parasite in the host. It has been shown in some studies that the risk of encountering an infected victim increases when there is a higher cannibalism rate, though this risk drops as the number of available hosts decreases. However, this is only the case if the risk of disease transmission is low. Cannibalism is an ineffective method of disease spread as cannibalism in the animal kingdom is normally a one-on-one interaction, and the spread of disease requires group cannibalism; thereby it is rare for a disease to have evolved to rely solely on cannibalism to spread. Usually there are different means of transmission, such as with direct contact, maternal transmission, coprophagy, and necrophagy with different species. Infected individuals are more likely to be consumed than non-infected individuals, thus some research has suggested that the spread of disease may be a limiting factor to the prevalence of cannibalism in the population.

Some examples of diseases transmitted by cannibalism in mammals include Kuru which is a prion disease that degenerates the brain. This disease was prevalent in Papua New Guinea where tribes practiced endocannibalism in cannibalistic funeral rituals and consume the brains infected by these prions. It is a cerebellar dysfunctional disease which has symptoms including a broad-based gait and decreased motor activity control; however, the disease has a long incubation period and symptoms may not appear until years later.

Bovine spongiform encephalopathy, or mad cow disease is another prion disease which is usually caused by feeding contaminated bovine tissue to other cattle. It is a neurodegenerative disease and could be spread to humans if the individual were to consume contaminated beef. The spread of parasites such as nematodes may also be facilitated by cannibalism as eggs from these parasites are transferred more easily from one host to another.

Other forms of diseases include sarcocystis and iridovirus in reptiles and amphibians; granulosus virus, chagas disease, and microsporidia in insects; stained prawn disease, white pot syndrome, helminthes and tapeworms in crustaceans and fish.

Foraging dynamics

Cannibalism may become apparent when direct competition for limited resources forces individuals to use other conspecific individuals as an additional resource to maintain their metabolic rates. Hunger drives individuals to increase their foraging rates, which in turn decreases their attack threshold and tolerance to other conspecific individuals. As resources dwindle, individuals are forced to change their behaviour which may lead to animal migration, confrontation, or cannibalism.

Cannibalism rates increase with increasing population density as it becomes more advantageous to prey on conspecific organisms than to forage in the environment. This is because the encounter rate between predator and prey increases, making cannibalism more convenient and beneficial than foraging within the environment. Over time, the dynamics within the population change as those with cannibalistic tendencies may receive additional nutritional benefits and increase the size ratio of predator to prey. The presence of smaller prey, or prey which are at a vulnerable stage of their life cycle, increases the chances of cannibalism occurring due to the reduced risk of injury. A feedback loop occurs when increasing rates of cannibalism decreases population densities, leading to an increased abundance of alternative food sources; making it more beneficial to forage within the environment than for cannibalism to occur. When population numbers and foraging rates increase, the carrying capacity for that resource in the area may be reached, thus forcing individuals to look for other resources such as conspecific prey.

Sexual cannibalism

Sexual cannibalism is present largely in spiders and other invertebrates, including gastropods. This refers to the killing and consumption of conspecific sexual partners during courtship, and during or after copulation. Normally, it is the female which consumes the conspecific male organism, though there have been some reported cases of the male consuming the adult female, however, this has only been recorded under laboratory conditions. Sexual cannibalism has been recorded in the female redback spider, black widow spider, praying mantis, and scorpion, among others.

In most species of spiders, the consumption of the male individual occurs before copulation and the male fails to transfer his sperm into the female. This may be due to mistaken identity such as in the case of the orb weaving spider which holds little tolerance to any spider which is present in its web and may mistake the vibrations for those of a prey item. Other reasons for male consumption before mating may include female choice and the nutritional advantages of cannibalism. The size of the male spider may play a part in determining its reproductive success as smaller males are less likely to be consumed during pre-copulation; however, larger males may be able to prevent the smaller ones from gaining access to the female. There exists a conflict of interest between males and females, as females may be more inclined to turn to cannibalism as a source of nutritional intake while the male's interest is mostly focused on ensuring paternity of the future generations. It was found that cannibalistic females produced offspring with greater survival rates than non-cannibalistic females, as cannibals produced greater clutches and larger egg sizes. Hence, species such as the male dark fishing spider of the family Dolomedes self-sacrifice and spontaneously die during copulation to facilitate their own consumption by the female, thereby increasing the chance of survivorship of future offspring.

Sexual dimorphism has been theorised to have arisen from sexual selection as smaller males were captured more easily than larger males; however, it is also possible that sexual cannibalism only occurs due to the difference in size between male and females. Data comparing female and male spider body length shows that there is little support for the prior theory as there is not much correlation between body size and the presence of sexual cannibalism. Not all species of spiders which partake in sexual cannibalism exhibit size dimorphism.

The avoidance of sexual cannibalism is present in males of certain species to increase their rate of survival, whereby the male uses cautionary methods to lower the risk of his consumption. Male orb weaving spiders would often wait for females to moult or to finish eating before attempting to initiate mating, as the females are less likely to attack. Males which are vulnerable to post-copulation consumption may gather mating thread to generate a mechanical tension which they could use to spring away after insemination, while other spiders such as the crab spider may tangle the female's legs in webs to reduce the risk of the female capturing him. Male choice is common in mantids whereby males were observed to choose fatter females due to the reduced risk of attack and were more hesitant to approach starved females.

Size-structured cannibalism

Size-structured cannibalism is cannibalism in which older, larger, more mature individuals consume smaller, younger conspecifics. In size-structured populations, (where populations are made of individuals of various sizes, ages, and maturities), cannibalism can be responsible for 8% (Belding's ground squirrel) to 95% (dragonfly larvae) of the total mortality, making it a significant and important factor for population and community dynamics.

Size-structured cannibalism has commonly been observed in the wild for a variety of taxa. Vertebrate examples include chimpanzees, where groups of adult males have been observed to attack and consume infants.

Filial cannibalism

Filial cannibalism is a specific type of size-structured cannibalism in which adults eat their own offspring. Although most often thought of as parents eating live young, filial cannibalism includes parental consumption of stillborn infants and miscarried fetuses as well as infertile and still-incubating eggs. Vertebrate examples include pigs, where savaging accounts for a sizable percentage of total piglet deaths, and cats.

Filial cannibalism is particularly common in teleost fishes, appearing in at least seventeen different families of teleosts. Within this diverse group of fish, there have been many, variable explanations of the possible adaptive value of filial cannibalism. One of these is the energy-based hypothesis, which suggests that fish eat their offspring when they are low on energy as an investment in future reproductive success. This has been supported by experimental evidence, showing that male three-spined sticklebacks, male tessellated darters, and male sphinx blenny fish all consume or absorb their own eggs to maintain their physical conditions. In other words, when males of a fish species are low on energy, it might sometimes be beneficial for them to feed on their own offspring to survive and invest in future reproductive success.

Another hypothesis as to the adaptive value of filial cannibalism in teleosts is that it increases density-dependent egg survivorship. In other words, filial cannibalism simply increases overall reproductive success by helping the other eggs make it to maturity by thinning out the numbers. Possible explanations as to why this is so include increasing oxygen availability to the remaining eggs, the negative effects of accumulating embryo waste, and predation.

In some species of eusocial wasps, such as Polistes chinensis, the reproducing female will kill and feed younger larvae to her older brood. This occurs under food stressed conditions in order to ensure that the first generation of workers emerges without delay. Further evidence also suggests that occasionally filial cannibalism might occur as a by-product of cuckoldry in fish. Males consume broods, which may include their own offspring, when they believe a certain percentage of the brood contains genetic material that is not theirs.

It is not always the parent that cannibalizes the offspring; in some spiders, mothers have been observed to feed themselves to their brood as the ultimate provision from mother to children, known as matriphagy.

The dinosaur Coelophysis was once suspected to practice this form of cannibalism but this turned out to be wrong, although Deinonychus may have done so. Skeletal remains from subadults with missing parts are suspected of having been eaten by other Deinonychus, mainly full-grown adults.

Infanticide

Infanticide is the killing of a non-adult animal by an adult of the same species. Infanticide is often accompanied by cannibalism. It is often displayed in lions; a male lion encroaching on the territory of a rival pride will often kill any existing cubs fathered by other males; this brings the lionesses into heat more quickly, enabling the invading lion to sire his own young. This is an example of cannibalistic behaviour in a genetic context.

In many species of Lepidoptera, such as Cupido minimus and the Indian mealmoth, the first larvae to hatch will consume the other eggs or smaller larvae on the host plant, decreasing competition.

Intrauterine cannibalism

Intrauterine cannibalism is a behaviour in some carnivorous species, in which multiple embryos are created at impregnation, but only one or two are born. The larger or stronger ones consume their less-developed siblings as a source of nutrients.

In adelphophagy or embryophagy, the fetus eats sibling embryos, while in oophagy it feeds on eggs.

Adelphophagy occurs in some marine gastropods (calyptraeids, muricids, vermetids, and buccinids) and in some marine annelids (Boccardia proboscidia in Spionidae).

Intrauterine cannibalism is known to occur in lamnoid sharks such as the sand tiger shark, and in the fire salamander, as well as in some teleost fishes. The Carboniferous period chimaera, Delphyodontos dacriformes, is suspected of having practiced intrauterine cannibalism, also, due to the sharp teeth of the recently born (or possibly aborted) juveniles, and the presence of fecal matter in the juveniles' intestines.

Protection against cannibalism

Animals have evolved protection to prevent and deter potential predators such as those from their own kind. Many amphibian eggs are gelatinous and toxic to decrease edibility. Often, adults would lay their eggs in crevices, holes, or empty nesting sites to hide their eggs from potential conspecific predators which tend to ingest the eggs for an additional nutritional benefit or to get rid of genetic competition. In amphibians, the development of non-aquatic egg deposition has helped increase the survival rates of their young by the evolution of viviparity or direct development. In bees, worker policing occurs to prohibit worker reproduction, whereby workers cannibalize other worker laid eggs. Queen laid eggs have a different scent than worker laid eggs, allowing workers to differentiate between the two, allowing them to nurture and protect queen laid eggs rather than cannibalising them. Parental presence at nesting sites is also a common method of protection against infanticide committed by conspecific individuals, whereby the parent exhibits defensive displays to ward off potential predators. Parental investment in newborns are generally higher during their early stages of development whereby behaviours such as aggression, territorial behaviour, and pregnancy blocking become more apparent.

Morphological plasticity helps an individual account for different predation stresses, thereby increasing individual survival rates. Japanese brown frog tadpoles have been shown to exhibit morphological plasticity when they are in a high stress environment where cannibalism between tadpoles and more developed individuals were present. Shifting their morphology plays a key role in their survival, creating bulkier bodies when put into environments where more developed tadpoles were present, to make it difficult for the individuals to swallow them whole. Diet shifts between different stages of development have also evolved to decrease competition between each stage, thereby increasing the amount of food availability so that there is a decreased chance that the individuals will turn to cannibalism as an additional food source.

Cannibalism in the media

Cannibalism has been a subject for horror movies since the 1980s. This genre is called cannibal films. In Planet Dinosaur it shows two Majungasaurus fighting to eat each other.

Cannibalism has also been a subject of video games. More recently, cannibalism has been featured in a positive light, with video games like Ark: Survival Evolved incentivizing players' virtual characters to eat each other.

Public health genomics

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Public_health_genomics

Public health genomics is the use of genomics information to benefit public health. This is visualized as more effective preventive care and disease treatments with better specificity, tailored to the genetic makeup of each patient. According to the Centers for Disease Control and Prevention (U.S.), Public Health genomics is an emerging field of study that assesses the impact of genes and their interaction with behavior, diet and the environment on the population's health.

This field of public health genomics is less than a decade old. A number of think tanks, universities, and governments (including the U.S., UK, and Australia) have started public health genomics projects. Research on the human genome is generating new knowledge that is changing public health programs and policies. Advances in genomic sciences are increasingly being used to improve health, prevent disease, educate and train the public health workforce, other healthcare providers, and citizens.

Public policy

Public policy has protected people against genetic discrimination, defined in Taber's Cyclopedic Medical Dictionary (2001) as unequal treatment of persons with either known genetic abnormalities or the inherited propensity for disease; genetic discrimination may have a negative effect on employability, insurability and other socio-economic variables. Public policy in the U.S. that protect individuals and groups of people against genetic discrimination include the Americans with Disabilities Act of 1990, Executive Order 13145 (2000) that prohibits genetic discrimination in the workplace for federal employees, and the Genetic Information Nondiscrimination Act of 2008.

Main public concerns regarding genomic information are that of confidentiality, misuse of information by health plans, employers, and medical practitioners, and the right of access to genetic information. Concerns also exist about the equitable deployment of public health genomics, and attention is needed to ensure that the implementation of genomic medicine does not further entrench social‐equity concerns.

Ethical concerns

One of the many facets involved in public health genomics is that of bioethics. This has been highlighted in a study in 2005 by Cogent Research, that found when American citizens were asked what they thought the strongest drawback was in using genetic information, they listed "misuse of information/invasion of privacy" as the single most important problem. In 2003, the Nuffield Council on Bioethics published a report, Pharmacogenetics: Ethical Issues. Authors of the document explore four broad categories of ethical and policy issues related to pharmacogenetics: information, resource, equity and control. In the introduction to the report, the authors clearly state that the development and application of pharmacogenetics depend on scientific research, but that policy and administration must provide incentives and restraints to ensure the most productive and just use of this technology. Involving the public in ethical oversight and other ways can improve public trust in public health genomics as well as acceptability of initiatives and ensuring that access to the benefits of genomics research is equitable.

Genetic susceptibility to disease

Single nucleotide polymorphisms (SNPs) are single bases within a gene sequence that differ from that gene's consensus sequence, and are present in a subset of the population. SNPs may have no effect on gene expression, or they can change the function of a gene completely. Resulting gene expression changes can, in some cases, result in disease, or in susceptibility to disease (e.g., viral or bacterial infection).

Some current tests for genetic diseases include: cystic fibrosis, Tay–Sachs disease, amyotrophic lateral sclerosis (ALS), Huntington's disease, high cholesterol, some rare cancers and an inherited susceptibility to cancer. A select few are explored below.

Herpesvirus and bacterial infections

Since the field of genomics takes into account the entire genome of an organism, and not simply its individual genes, the stud of latent viral infection falls into this realm. For example, the DNA of a latent herpesvirus integrates into the host's chromosome and propagates through cell replication, although it is not part of the organism's genome, and was not present at the birth of the individual.

An example of this is found in a study published in Nature, which showed that mice with a latent infection of a herpesvirus were less susceptible to bacterial infections. Murine mice were infected with murine gammaherpesvirus 68 and then challenged with the Listeria monocytogenes bacterium. Mice that had a latent infection of the virus had an increased resistance to the bacteria, but those with a non-latent strain of virus had no change in susceptibility to the bacteria. The study went on to test mice with murine cytomegalovirus, a member of the betaherpesvirinae subfamily, which provided similar results. However, infection with human herpes simplex virus type-1 (HSV-1), a member of the alphaherpesvirinae subfamily, did not provide increased resistance to bacterial infection. They also used Yersinia pestis (the causative agent of the Black Death) to challenge mice with a latent infection of gammaherpesvirus 68, and they found the mice did have an increased resistance to the bacteria. The suspected reason for this is that peritoneal macrophages in the mouse are activated after latent infection of the herpesvirus, and since macrophages play an important role in immunity, this provides the mouse with a stronger, active immune system at the time of bacterial exposure. It was found that the latent herpesvirus caused an increase in interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α), cytokines which both lead to activation of macrophages and resistance to bacterial infection.

Influenza and Mycobacterium tuberculosis

Variations within the human genome can be studied to determine susceptibility to infectious diseases. The study of variations within microbial genomes will also need to be evaluated to use genomics of infectious disease within public health. The ability to determine if a person has greater susceptibility to an infectious disease will be valuable to determine how to treat the disease if it is present or prevent the person from getting the disease. Several infectious diseases have shown a link between genetics and susceptibility in that families tend to have heritability traits of a disease.

During the course of the past influenza pandemics and the current influenza epizootic there has been evidence of family clusters of disease. Kandun, et al. found that family clusters in Indonesia in 2005 resulted in mild, severe and fatal cases among family members. The findings from this study raise questions about genetic or other predispositions and how they affect a person's susceptibility to and severity of disease. Continued research will be needed to determine the epidemiology of H5N1 infection and whether genetic, behavioral, immunologic, and environmental factors contribute to case clustering.

Host genetic factors play a major role in determining differential susceptibility to major infectious diseases of humans. Infectious diseases in humans appear highly polygenic with many loci implicated but only a minority of these convincingly replicated. Over the course of time, humans have been exposed to organisms like Mycobacterium tuberculosis. It is possible that the human genome has evolved in part from our exposure to M. tuberculosis. Animal model studies and whole genome screens can be used to identify potential regions on a gene that suggest evidence of tuberculosis susceptibility. In the case of M. tuberculosis, animal model studies were used to suggest evidence of a locus which was correlated with susceptibility, further studies were done to prove the link between the suggested locus and susceptibility. The genetic loci that have been identified as associated with susceptibility to tuberculosis are HLA-DR, INF-γ, SLC11A1, VDR, MAL/TIRAP, and CCL2. Further studies will be needed to determine genetic susceptibility to other infectious diseases and ways public health officials can prevent and test for these infections to enhance the concept of personalized medicine.

Type 1 Diabetes, immunomics, and public health

The term genomics, referring to the organism's whole genome, is also used to refer to gene informatics, or the collection and storage of genetic data, including the functional information associated with the genes, and the analysis of the data as combinations, patterns and networks by computer algorithms. Systems biology and genomics are natural partners, since the development of genomic information and systems naturally facilitates analysis of systems biology questions involving relationships between genes, their variants (SNPs) and biological function. Such questions include the investigation of signaling pathways, evolutionary trees, or biological networks, such as immune networks and pathways. For this reason, genomics and these approaches are particularly suited to studies in immunology. The study of immunology using genomics, as well as proteomics and transcriptomics (including gene profiles, either genomic or expressed gene mRNA profiles), has been termed immunomics.

Accurate and sensitive prediction of disease, or detection during early stages of disease, could allow the prevention or arrest of disease development as immunotherapy treatments become available. Type-1 diabetes markers associated with disease susceptibility have been identified, for example HLA class II gene variants, however possession of one or more of these genomic markers does not necessarily lead to disease. Lack of progression to disease is likely due to the absence of environmental triggers, absence of other susceptibility genes, presence of protective genes, or differences in the temporal expression or presence of these factors. Combinations of markers have also been associated with susceptibility to type-1 diabetes however again, their presence may not always predict disease development, and conversely, disease may be present without the marker group. Potential variant genes (SNPs) or markers that are linked to the disease include genes for cytokines, membrane-bound ligands, insulin and immune regulatory genes.

Meta-analyses have been able to identify additional associated genes, by pooling a number of large gene datasets. This successful study illustrates the importance of compiling and sharing large genome databases. The inclusion of phenotypic data in these databases will enhance discovery of candidate genes, while the addition of environmental and temporal data should be able to advance the disease progression pathways knowledge. HUGENet, which was initiated by the Centers for Disease Control and Prevention (U.S.), is accomplishing the integration of this type of information with the genome data, in a form available for analysis. This project could be thought of as an example of 'metagenomics', the analysis of a community's genome, but for a human rather than a microbial community. This project is intended to promote international data sharing and collaboration, in addition to creating a standard and framework for the collection of this data.

Nonsyndromic hearing loss

Variations within the human genome are being studied to determine susceptibility to chronic diseases, as well as infectious diseases. According to Aileen Kenneson and Coleen Boyle, about one sixth of the U.S. population has some degree of hearing loss. Recent research has linked variants in the gap junction beta 2 (GJB2) gene to nonsyndromic prelingual sensorineural hearing loss. GJB2 is a gene encoding for connexin, a protein found in the cochlea. Scientists have found over 90 variants in this gene and sequence variations may account for up to 50% of nonsyndromic hearing loss. Variants in GJB2 are being used to determine age of onset, as well as severity of hearing loss.

It is clear that there are also environmental factors to consider. Infections such as rubella and meningitis and low birth weight and artificial ventilation, are known risk factors for hearing loss, but perhaps knowing this, as well as genetic information, will help with early intervention.

Information gained from further research in the role of GJB2 variants in hearing loss may lead to newborn screening for them. As early intervention is crucial to prevent developmental delays in children with hearing loss, the ability to test for susceptibility in young children would be beneficial. Knowing genetic information may also help in the treatment of other diseases if a patient is already at risk.

Further testing is needed, especially in determining the role of GJB2 variants and environmental factors on a population level, however initial studies show promise when using genetic information along with newborn screening.

Genomics and health

Pharmacogenomics

The World Health Organization has defined pharmacogenomics as the study of DNA sequence variation as it relates to different drug responses in individuals, i.e., the use of genomics to determine an individual's response. Pharmacogenomics refers to the use of DNA-based genotyping in order to target pharmaceutical agents to specific patient populations in the design of drugs.

Current estimates state that 2 million hospital patients are affected by adverse drug reactions every year and adverse drug events are the fourth leading cause of death. These adverse drug reactions result in an estimated economic cost of $136 billion per year. Polymorphisms (genetic variations) in individuals affect drug metabolism and therefore an individual's response to a medication. Examples of ways in which genetics may affect an individual's response to drugs include: drug transporters, metabolism and drug interactions. Pharmacogenetics may be used in the near future by public health practitioners to determine the best candidates for certain drugs, thereby reducing much of the guesswork in prescribing drugs. Such actions have the potential to improve the effectiveness of treatments and reduce adverse drug events.

Nutrition and health

Nutrition is very important in determining various states of health. The field of nutrigenomics is based on the idea that everything ingested into a person's body affects the genome of the individual. This may be through either upregulating or downregulating the expression of certain genes or by a number of other methods. While the field is quite young there are a number of companies that market directly to the public and promote the issue under the guise of public health. Yet many of these companies claim to benefit the consumer, the tests performed are either not applicable or often result in common sense recommendations. Such companies promote public distrust towards future medical tests that may test more appropriate and applicable agents.

An example of the role of nutrition would be the methylation pathway involving methylene tetrahydrofolate reductase (MTHFR). An individual with the SNP may need increased supplementation of vitamin B12 and folate to override the effect of a variant SNP. Increased risk for neural tube defects and elevated homocysteine levels have been associated with the MTHFR C677T polymorphism.

In 2002, researchers from the Johns Hopkins Bloomberg School of Public Health identified the blueprint of genes and enzymes in the body that enable sulforaphane, a compound found in broccoli and other vegetables, to prevent cancer and remove toxins from cells. The discovery was made using a "gene chip," which allows researchers to monitor the complex interactions of thousands of proteins on a whole genome rather than one at time. This study was the first gene profiling analysis of a cancer-preventing agent using this approach. University of Minnesota researcher Sabrina Peterson, coauthored a study with Johanna Lampe of the Fred Hutchinson Cancer Research Center, Seattle, in October 2002 that investigated the chemoprotective effect of cruciferous vegetables (e.g., broccoli, brussels sprouts). Study results published in The Journal of Nutrition outline the metabolism and mechanisms of action of cruciferous vegetable constituents, discusses human studies testing effects of cruciferous vegetables on biotransformation systems and summarizes the epidemiologic and experimental evidence for an effect of genetic polymorphisms (genetic variations) in these enzymes in response to cruciferous vegetable intake.

Healthcare and genomics

Members of the public are continually asking how obtaining their genetic blueprint will benefit them, and why they find that they are more susceptible to diseases that have no cures.

Researchers have found that almost all disorders and diseases that affect humans reflect the interplay between the environment and their genes; however we are still in the initial stages of understanding the specific role genes play on common disorders and diseases. For example, while news reports may give a different impression, most cancer is not inherited. It is therefore likely that the recent rise in the rates of cancer worldwide can be at least partially attributed to the rise in the number of synthetic and otherwise toxic compounds found in our society today. Thus, in the near future, public health genomics, and more specifically environmental health, will become an important part of the future healthcare-related issues.

Potential benefits of uncovering the human genome will be focused more on identifying causes of disease and less on treating disease, through: improved diagnostic methods, earlier detection of a predisposing genetic variation, pharmacogenomics and gene therapy.

For each individual, the experience of discovering and knowing their genetic make-up will be different. For some individuals, they will be given the assurance of not obtaining a disease, as a result of familial genes, in which their family has a strong history and some will be able to seek out better medicines or therapies for a disease they already have. Others will find they are more susceptible to a disease that has no cure. Though this information maybe painful, it will give them the opportunity to prevent or delay the on-set of that disease through: increased education of the disease, making lifestyle changes, finding preventive therapies or identifying environmental triggers of the disease. As we continue to have advances in the study of human genetics, we hope to one day incorporate it into the day-to-day practice of healthcare. Understanding one's own genetic blueprint can empower oneself to take an active role in promoting their own health.

Genomics and understanding of disease susceptibility can help validate family history tool for use by practitioners and the public. IOM is validating the family history tool for six common chronic diseases (breast, ovarian, colorectal cancer, diabetes, heart disease, stroke) (IOM Initiative). Validating cost effective tools can help restore importance of basic medical practices (e.g. family history) in comparission to technology intensive investigations.

The genomic face of immune responses

A critical set of phenomena that ties together various aspects of health interventions, such as drug sensitivity screening, cancer or autoimmune susceptibility screening, infectious disease prevalence and application of pharmacologic or nutrition therapies, is the systems biology of the immune response. For example, the influenza epidemic of 1918, as well as the recent cases of human fatality due to H5N1 (avian flu), both illustrate the potentially dangerous sequence of immune responses to this virus. Also well documented is the only case of spontaneous "immunity" to HIV in humans, shown to be due to a mutation in a surface protein on CD4 T cells, the primary targets of HIV. The immune system is truly a sentinel system of the body, with the result that health and disease are carefully balanced by the modulated response of each of its various parts, which then also act in concert as a whole. Especially in industrialized and rapidly developing economies, the high rate of allergic and reactive respiratory disease, autoimmune conditions and cancers are also in part linked to aberrant immune responses that are elicited as the communities' genomes encounter swiftly changing environments. The causes of perturbed immune responses run the gamut of genome-environment interactions due to diet, supplements, sun exposure, workplace exposures, etc. Public health genomics as a whole will absolutely require a rigorous understanding of the changing face of immune responses.

Newborn screening

The experience of newborn screening serves as the introduction to public health genomics for many people. If they did not undergo prenatal genetic testing, having their new baby undergo a heel stick in order to collect a small amount of blood may be the first time an individual or couple encounters genetic testing. Newborn genetic screening is a promising area in public health genomics that appears poised to capitalize on the public health goal of disease prevention as a primary form of treatment.

Most of the diseases that are screened for are extremely rare, single-gene disorders that are often autosomal recessive conditions and are not readily identifiable in neonates without these types of tests. Therefore, often the treating physician has never seen a patient with the disease or condition and so an immediate referral to a specialty clinic is necessary for the family.

Most of the conditions identified in newborn screening are metabolic disorders that either involve i) lacking an enzyme or the ability to metabolize (or breakdown) a particular component of the diet, like phenylketonuria, ii) abnormality of some component of the blood, especially the hemoglobin protein, or iii) alteration of some component of the endocrine system, especially the thyroid gland. Many of these disorders, once identified, can be treated before more severe symptoms, such as mental retardation or stunted growth, set in.

Newborn genetic screening is an area of tremendous growth. In the early 1960s, the only test was for phenylketonuria. In 2000, roughly two-thirds of states in the US screened for 10 or fewer genetic diseases in newborns. Notably, in 2007, 95% of states in the US screen for more than 30 different genetic diseases in newborns. Especially as costs have come down, newborn genetic screening offers "an excellent return on the expenditure of public health dollars".

Because the risks and benefits of genomic sequencing for newborns are still not fully understood, the BabySeq Project, led by Robert C. Green of Brigham and Women's Hospital and Alan H. Beggs of Boston Children's Hospital (BCH) has been gathering critical research on newborn sequencing since 2015 as part of the Newborn Sequencing In Genomic medicine and public HealTh consortium (NSIGHT), which received a five-year grant of $25 million from the National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI).

Understanding traditional healing practices

Genomics will help develop an understanding of the practices that have evolved over centuries in old civilizations and which have been strengthened by observations (phenotype presentations) from generation to generation, but which lack documentation and scientific evidence. Traditional healers associated specific body types with resistance or susceptibility to particular diseases under specific conditions. Validation and standardization of this knowledge/ practices has not yet been done by modern science. Genomics, by associating genotypes with the phenotypes on which these practices were based, could provide key tools to advance the scientific understanding of some of these traditional healing practices.

Youth suicide

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Youth_suicide

Youth suicide is when a young person, generally categorized as someone below the legal age of majority, deliberately ends their own life. Rates of youth suicide and attempted youth suicide in Western societies and other countries are high. Youth suicide attempts are more common among girls, but adolescent males are the ones who usually carry out suicide. Suicide rates in youths have nearly tripled between the 1960s and 1980s. For example, in Australia suicide is second only to motor vehicle accidents as its leading cause of death for people aged 15 to 25.

In the U.S., according to the National Institute of Mental Health, the suicide rate is the 2nd leading cause of death for adolescents between the ages of 10 and 14, and the third leading cause of death for those between 15 and 19. In 2021, the American Academy of Pediatrics, the American Academy of ChiId and Adolescent Psychiatry, and the Children's Hospital Association released a joint statement announcing a mental health crisis among our youth. Emergency room visits for mental health issues have dramatically increased, especially after the COVID-19 pandemic.

Suicide contagion

According to research conducted by the Commission for Children and Young People and Child Guardian in 2007, 39% of all youth suicides are completed by young people who have lost someone of influence / significance to them to suicide. The Commission terms this suicide contagion and makes several recommendations as to the importance of safeguarding young people and communities from suicide contagion.

In 2011 the Australian Federal Parliament Standing Committee for Health and Ageing Inquiry into Youth Suicide met in a round table forum with young representatives from three organizations at the forefront of preventing youth suicide. These organizations included Sunnykids, Inspire, and Boys Town. The Standing Committee has since released a discussion paper highlighting the findings of their inquiry and will seek to make final recommendations on the most effective means for reducing youth suicide.

Teens at risk

One of the problems facing teenagers at risk of suicide is getting psychiatric counselling when it is needed. One research at the beginning of 2020 shows that compared with older adolescents, younger adolescents particularly agree that increased cyberbullying and despair are very important factors influencing suicide among adolescents. One study says, "In teenagers, depression is considered a major – if not the leading – cause of teen suicide." Factors and risks contributed to youth suicide are academic pressure, alcohol consumption, the loss of a valued relationship, frequent change of residency, and poor family patterns. Harassment is a leading cause of teen suicide, along with abuse. Gay teens or those unsure of their sexual identity are more likely to die by suicide, particularly if they have suffered bullying or harassment, as discussed next. The following campaigns have been started in hopes of giving teens hope and abolishing the feeling of isolation.

It Gets Better
Born This Way
I Get Bullied Too
Stop Youth Suicide

Lack of impulse control has been found to differentiate adolescent suicide attempters from a control group of adolescents with an acute illness (Slap, Vorters, Chaudhuri, & Centor, 1988). However, impulsivity does not characterize all suicide attempters, since group comparisons have found no differences between suicidal patients and psychiatric controls on a measure of cognitive impulsivity (Patsiokas, Clum, & Luscomb, 1979). Instead, impulsivity may be important in identifying high-risk subgroups.

Sexual minority youth and suicide

Youth that fall under the category of sexual minorities are at an elevated risk of depression and succumbing to self-harm. Among the population of sexual minority youth, on average, 28% explain having past experiences with suicidal actions and/or thoughts. Lesbian and gay youth are the group most likely to face negative experiences, leading to a higher likelihood of the development of suicidal thoughts according to mental care professionals. Bisexuality also carries a higher likelihood of suicidality with bisexuals being five times more likely to report suicidal thoughts and actions. Sexual minority youth also report a higher incidence of substance abuse when compared to heterosexuals. Overall, studies suggest that sexual minority youth carry a higher incidence of suicide and depression, and that reforms centered on alleviating minority stigma attenuate this disparity.

Previous exposure, attempts, and age impacting youth suicide

Exposure to suicide, previous attempts of suicide, and age are some of the most influential factors of young individuals and their probability of dying by suicide. Adolescent exposure to suicide through classmates has caused researchers to hypothesize suicide as a contagion. They note how a child's exposure to suicide predicts suicide ideation and attempts. Previous exposure to suicide through parental attempts have also been found to have a 3.5% increase in a youth's probability of having suicidal thoughts, with a 2.6% increased chance of them attempting suicide. Aggression in families and its transference can be one of the main causes of transmission of suicidal tendencies in families.

Previous attempts of suicide also play a major role in a youth attempting suicide again. On average, it has been recorded that the follow-up period for suicide-attempters was 3.88 years. Evidence shows those most at risk for suicide are those who previously attempted suicide, with research showing that they can have anywhere from a 40 to over a 100 times higher chance of dying by suicide compared to the general population.

Age and experience also factor in suicide. It has been found that older, more experienced populations take more time to plan, choose deadlier methods, and have greater suicidal intent. This results in them eventually committing suicide at a higher rate than their younger counterparts.

Bereavement among young people

The primary goals of suicide postvention include assisting the survivors of suicide with the grief process, along with identifying and referring those survivors who may be at risk for negative outcomes such as depressive and anxiety disorders, and suicidal behaviour. With 42% of youth suicides being suicide bereavement (or contagion) related – further research and investment must be made into supporting this group of people. A few suggestions to make sure the support is effective include making the individuals feel connected and understood.

Epidemiology

Two possible determinants to suicide attempts are lifetime sexual abuse and adult physical violence. Among participants aged 18–25, the odds ratios for lifetime sexual abuse and adult physical violence are 4.27 and 3.85, respectively. In other words, those who died by suicide are 327% more likely to have experienced lifetime sexual assault. Similarly, a suicide victim is 285% more likely to have suffered physical violence as an adult. Based on a survey done on American high school students, 16% reported considering suicide and 8% reported attempting suicide sometime within the 12 months before taking the survey. Between 1980 and 1994, the suicide rates of young black males doubled. American Indians and Alaska Natives die by suicide at a higher rate than any other ethnic group in the United States. In India, one-third of suicides are young people 15–29. In 2002, 154,000 suicides were recorded in India. In the United States, about 60 percent of suicides are carried out with a gun. Some Aboriginal teens and gay or lesbian teens are at high risk, depending on their community and their own self-esteem. Several campaigns have been started to give them hope and help them to feel less isolated.

The 2019 Youth Risk Behavior Survey, which was conducted by the CDC, found that between 2009 and 2018, suicide rates among adolescents aged 14-18 years increased by 61.7%. Furthermore, the CDC reported that in 2019, among American adolescents in grades 9 to12:

18.8% of students reported seriously considering attempting suicide
15.7% of students made a suicide plan
8.9% of students attempted suicide

Intervention

One organization in Australia has found that young people who feel connected, supported, and understood are less likely to die by suicide. Reports on the attitudes of young people identified as at risk of suicide have been released. Such reports support the notion that connectedness, a sense of being supported and respected, is a protective factor for young people at risk of suicide. According to Pueblo Suicide Prevention Center (PSPC) for some reason kids today are experiencing more pressure.

For immediate help, contact SAMHSA's National Suicide Prevention Lifeline at 1-800-273-TALK (8255).

Issues for communities

Intervention issues for communities to address include suicide contagion, developmental understanding of suicide, development and suicide risk, and the influence of culture. Key matters in postvention responses for young people include: community context, life stage relevance of responses, identification, and referral (Postvention Co-ordination), developing a suite of services, and creating ongoing options.

Prevention

One can help prevent adolescent suicide by discouraging isolation, addressing a child's depression which is correlated with suicide, getting rid of any objects that a child could use to attempt suicide, and simply paying attention to what the child does or feels.

Schools are a great place to provide more education and support for suicide prevention. Since students spend the majority of their time at school, the school can be either a haven from or a source of suicidal triggers, and students' peers can heavily influence their state of mind. The school setting is an ideal environment to educate students on suicide and have support readily available.

Suicide Prevention Resource Center provides professional information and resources on suicide prevention.

Prevention resources for parents, guardians, social workers, teachers, school staff, peers:

Sibshops
Youth Mental Health First Aid
More can be found on U.S. Department of Health & Human Services website for Mental Health in Adolescent

National Suicide Prevention Lifeline for Youth provides resources and information for teens and adolescents such as:

The Trevor Project
You Matter
StopBullying.gov
Love is Respect
Ditch the Label

Table of youth suicide rates (per 100,000)

Country	Year of Data	Rate of Males	Rate of Females	Total
Sri Lanka	1986	43.9	49.3	46.5
Lithuania	2002	38.4	8.8	23.9
Russian Federation	2002	38.5	8.3	23.6
Kazakhstan	2002	31.2	10.5	21.0
Luxembourg	2002	23.5	8.2	16.0
New Zealand	2000	22.3	8.2	15.3
El Salvador	1993	13.2	15.8	14.5
Belarus	2001	23.6	3.9	14.0
Estonia	2002	24.1	1.9	13.2
Turkmenistan	1998	16.6	8.8	12.8
Ukraine	2000	19.6	4.9	12.4
Ireland	2000	19.8	4.3	12.3
Mauritius	2000	10.1	12.5	11.3
Norway	2001	15.3	6.2	10.9
Canada	2000	16.3	5.2	10.8
Latvia	2002	16.9	4.4	10.8
Kyrgyzstan	2002	15.2	4.8	10.0
Austria	2002	15.1	3.8	9.6
Trinidad and Tobago	1994	8.9	10.5	9.6
Finland	2002	15.0	3.8	9.5
Uzbekistan	2000	12.5	6.4	9.5
Belgium	1997	14.5	3.9	9.3
Cuba	1996	6.1	12.5	9.2
Ecuador	1991	6.9	11.4	9.1
Australia	2001	13.8	3.8	8.9
Singapore	2001	9.2	7.8	8.5
Poland	2001	14.1	2.4	8.4
Switzerland	2000	12.6	4.0	8.4
Croatia	2002	14.0	2.1	8.2
USA	2000	13.0	2.7	8.0
Slovenia	1987	12.0	3.1	7.6
Hungary	2002	11.2	3.8	7.5
Japan	2000	8.8	3.8	6.4
Uruguay	1990	8.3	3.9	6.2
Bulgaria	2002	9.2	2.3	5.8
Czech Republic	2001	9.5	1.8	5.7
Argentina	1996	7.1	4.0	5.6
Costa Rica	1995	7.1	4.0	5.6
Germany	2001	8.7	2.4	5.6
Thailand	1994	6.1	5.1	5.6
Colombia	1994	6.7	4.2	5.5
Venezuela	1994	7.1	3.8	5.5
Republic of Korea	2001	5.9	4.9	5.4
Hong Kong	1999	5.1	5.3	5.2
France	1999	7.5	2.5	5.0
Denmark	1999	9.0	0.7	4.9
Israel	1999	8.7	0.0	4.9
Romania	2002	7.0	2.2	4.7
Netherlands	2000	7.4	1.8	4.6
Sweden	2001	5.7	2.8	4.3
Brazil*	1995	5.7	2.6	4.2
Puerto Rico	1992	8.3	0.0	4.2
United Kingdom	1999	6.5	1.8	4.2
Republic of Moldova	2002	7.1	1.1	4.1
China*	1999	3.2	4.8	4.0
Slovakia	2002	5.8	1.9	3.9
Chile	1994	6.2	1.3	3.8
Mexico	1995	5.1	2.3	3.7
Spain	2000	5.3	1.4	3.4
Panama	1987	4.6	1.6	3.1
Albania	2001	2.8	3.3	3.0
Dominican Republic	1985	2.7	3.2	2.9
Italy	2000	3.6	1.7	2.7
Macedonia	2000	1.2	3.7	2.4
Tajikistan	1999	3.3	0.9	2.1
Portugal	2000	2.6	0.9	1.8
Greece	1999	2.7	0.6	1.7
Peru	1983	1.3	0.7	1.0

Information taken from World Psychiatry, the official journal of the World Psychiatric Association. Numbers are per 100,000.

Bioluminescence

From Wikipedia, the free encyclopedia

Video of a bioluminescent beetle Elateroidea

Bioluminescence is the production and emission of light by living organisms. It is a form of chemiluminescence. Bioluminescence occurs widely in marine vertebrates and invertebrates, as well as in some fungi, microorganisms including some bioluminescent bacteria, and terrestrial arthropods such as fireflies. In some animals, the light is bacteriogenic, produced by symbiotic bacteria such as those from the genus Vibrio; in others, it is autogenic, produced by the animals themselves.

In a general sense, the principal chemical reaction in bioluminescence involves a light-emitting molecule and an enzyme, generally called luciferin and luciferase, respectively. Because these are generic names, luciferins and luciferases are often distinguished by the species or group, e.g. firefly luciferin. In all characterized cases, the enzyme catalyzes the oxidation of the luciferin.

In some species, the luciferase requires other cofactors, such as calcium or magnesium ions, and sometimes also the energy-carrying molecule adenosine triphosphate (ATP). In evolution, luciferins vary little: one in particular, coelenterazine, is found in 11 different animal phyla, though in some of these, the animals obtain it through their diet. Conversely, luciferases vary widely between different species, which is evidence that bioluminescence has arisen over 40 times in evolutionary history.

Both Aristotle and Pliny the Elder mentioned that damp wood sometimes gives off a glow. Many centuries later Robert Boyle showed that oxygen was involved in the process, in both wood and glowworms. It was not until the late nineteenth century that bioluminescence was properly investigated. The phenomenon is widely distributed among animal groups, especially in marine environments. On land it occurs in fungi, bacteria and some groups of invertebrates, including insects.

The uses of bioluminescence by animals include counterillumination camouflage, mimicry of other animals, for example to lure prey, and signaling to other individuals of the same species, such as to attract mates. In the laboratory, luciferase-based systems are used in genetic engineering and biomedical research. Researchers are also investigating the possibility of using bioluminescent systems for street and decorative lighting, and a bioluminescent plant has been created.

History

Before the development of the safety lamp for use in coal mines, dried fish skins were used in Britain and Europe as a weak source of light. This experimental form of illumination avoided the necessity of using candles which risked sparking explosions of firedamp. Another safe source of illumination in mines was bottles containing fireflies. In 1920, the American zoologist E. Newton Harvey published a monograph, The Nature of Animal Light, summarizing early work on bioluminescence. Harvey notes that Aristotle mentions light produced by dead fish and flesh, and that both Aristotle and Pliny the Elder (in his Natural History) mention light from damp wood. He also records that Robert Boyle experimented on these light sources, and showed that both they and the glowworm require air for light to be produced. Harvey notes that in 1753, J. Baker identified the flagellate Noctiluca "as a luminous animal" "just visible to the naked eye", and in 1854 Johann Florian Heller (1813–1871) identified strands (hyphae) of fungi as the source of light in dead wood.

Tuckey, in his posthumous 1818 Narrative of the Expedition to the Zaire, described catching the animals responsible for luminescence. He mentions pellucids, crustaceans (to which he ascribes the milky whiteness of the water), and cancers (shrimps and crabs). Under the microscope he described the "luminous property" to be in the brain, resembling "a most brilliant amethyst about the size of a large pin's head".

Charles Darwin noticed bioluminescence in the sea, describing it in his Journal:

While sailing in these latitudes on one very dark night, the sea presented a wonderful and most beautiful spectacle. There was a fresh breeze, and every part of the surface, which during the day is seen as foam, now glowed with a pale light. The vessel drove before her bows two billows of liquid phosphorus, and in her wake she was followed by a milky train. As far as the eye reached, the crest of every wave was bright, and the sky above the horizon, from the reflected glare of these livid flames, was not so utterly obscure, as over the rest of the heavens.

Darwin also observed a luminous "jelly-fish of the genus Dianaea", noting that: "When the waves scintillate with bright green sparks, I believe it is generally owing to minute crustacea. But there can be no doubt that very many other pelagic animals, when alive, are phosphorescent." He guessed that "a disturbed electrical condition of the atmosphere" was probably responsible. Daniel Pauly comments that Darwin "was lucky with most of his guesses, but not here", noting that biochemistry was too little known, and that the complex evolution of the marine animals involved "would have been too much for comfort".

Osamu Shimomura isolated the photoprotein aequorin and its cofactor coelenterazine from the crystal jelly *Aequorea victoria* in 1961.

Bioluminescence attracted the attention of the United States Navy in the Cold War, since submarines in some waters can create a bright enough wake to be detected; a German submarine was sunk in the First World War, having been detected in this way. The navy was interested in predicting when such detection would be possible, and hence guiding their own submarines to avoid detection.

Among the anecdotes of navigation by bioluminescence is one recounted by the Apollo 13 astronaut Jim Lovell, who as a navy pilot had found his way back to his aircraft carrier USS Shangri-La when his navigation systems failed. Turning off his cabin lights, he saw the glowing wake of the ship, and was able to fly to it and land safely.

The French pharmacologist Raphaël Dubois carried out work on bioluminescence in the late nineteenth century. He studied click beetles (Pyrophorus) and the marine bivalve mollusc Pholas dactylus. He refuted the old idea that bioluminescence came from phosphorus, and demonstrated that the process was related to the oxidation of a specific compound, which he named luciferin, by an enzyme. He sent Harvey siphons from the mollusc preserved in sugar. Harvey had become interested in bioluminescence as a result of visiting the South Pacific and Japan and observing phosphorescent organisms there. He studied the phenomenon for many years. His research aimed to demonstrate that luciferin, and the enzymes that act on it to produce light, were interchangeable between species, showing that all bioluminescent organisms had a common ancestor. However, he found this hypothesis to be false, with different organisms having major differences in the composition of their light-producing proteins. He spent the next 30 years purifying and studying the components, but it fell to the young Japanese chemist Osamu Shimomura to be the first to obtain crystalline luciferin. He used the sea firefly Vargula hilgendorfii, but it was another ten years before he discovered the chemical's structure and published his 1957 paper Crystalline Cypridina Luciferin. Shimomura, Martin Chalfie, and Roger Y. Tsien won the 2008 Nobel Prize in Chemistry for their 1961 discovery and development of green fluorescent protein as a tool for biological research.

Harvey wrote a detailed historical account on all forms of luminescence in 1957. An updated book on bioluminescence covering also the twentieth and early twenty-first century was published recently.

Evolution

In 1932 E. N. Harvey was among the first to propose how bioluminescence could have evolved. In this early paper, he suggested that proto-bioluminescence could have arisen from respiratory chain proteins that hold fluorescent groups. This hypothesis has since been disproven, but it did lead to considerable interest in the origins of the phenomenon. Today, the two prevailing hypotheses (both concerning marine bioluminescence) are those put forth by Howard Seliger in 1993 and Rees et al. in 1998.

Seliger's theory identifies luciferase enzymes as the catalyst for the evolution of bioluminescent systems. It suggests that the original purpose of luciferases was as mixed-function oxygenases. As the early ancestors of many species moved into deeper and darker waters natural selection favored the development of increased eye sensitivity and enhanced visual signals. If selection were to favor a mutation in the oxygenase enzyme required for the breakdown of pigment molecules (molecules often associated with spots used to attract a mate or distract a predator) it could have eventually resulted in external luminescence in tissues.

Rees et al. use evidence gathered from the marine luciferin coelenterazine to suggest that selection acting on luciferins may have arisen from pressures to protect oceanic organisms from potentially deleterious reactive oxygen species (e.g. H₂O₂ and O₂⁻ ). The functional shift from antioxidation to bioluminescence probably occurred when the strength of selection for antioxidation defense decreased as early species moved further down the water column. At greater depths exposure to ROS is significantly lower, as is the endogenous production of ROS through metabolism.

While popular at first, Seliger's theory has been challenged, particularly on the biochemical and genetic evidence that Rees examines. What remains clear, however, is that bioluminescence has evolved independently at least 40 times. Bioluminescence in fish began at least by the Cretaceous period. About 1,500 fish species are known to be bioluminescent; the capability evolved independently at least 27 times. Of these, 17 involved the taking up of bioluminous bacteria from the surrounding water while in the others, the intrinsic light evolved through chemical synthesis. These fish have become surprisingly diverse in the deep ocean and control their light with the help of their nervous system, using it not just to lure prey or hide from predators, but also for communication.

All bioluminescent organisms have in common that the reaction of a "luciferin" and oxygen is catalyzed by a luciferase to produce light. McElroy and Seliger proposed in 1962 that the bioluminescent reaction evolved to detoxify oxygen, in parallel with photosynthesis.

Thuesen, Davis et al. showed in 2016 that bioluminescence has evolved independently 27 times within 14 fish clades across ray-finned fishes.

Chemical mechanism

Bioluminescence is a form of chemiluminescence where light energy is released by a chemical reaction. This reaction involves a light-emitting pigment, the luciferin, and a luciferase, the enzyme component. Because of the diversity of luciferin/luciferase combinations, there are very few commonalities in the chemical mechanism. From currently studied systems, the only unifying mechanism is the role of molecular oxygen; often there is a concurrent release of carbon dioxide (CO₂). For example, the firefly luciferin/luciferase reaction requires magnesium and ATP and produces CO₂, adenosine monophosphate (AMP) and pyrophosphate (PP) as waste products. Other cofactors may be required, such as calcium (Ca²⁺) for the photoprotein aequorin, or magnesium (Mg²⁺) ions and ATP for the firefly luciferase. Generically, this reaction can be described as:

Luciferin + O₂

\to_{other cofactors}^{Luciferase}

Oxyluciferin + light energy

Coelenterazine is a luciferin found in many different marine phyla from comb jellies to vertebrates. Like all luciferins, it is oxidised to produce light.

Instead of a luciferase, the jellyfish Aequorea victoria makes use of another type of protein called a photoprotein, in this case specifically aequorin. When calcium ions are added, rapid catalysis creates a brief flash quite unlike the prolonged glow produced by luciferase. In a second, much slower step, luciferin is regenerated from the oxidized (oxyluciferin) form, allowing it to recombine with aequorin, in preparation for a subsequent flash. Photoproteins are thus enzymes, but with unusual reaction kinetics. Furthermore, some of the blue light released by aequorin in contact with calcium ions is absorbed by a green fluorescent protein, which in turn releases green light in a process called resonant energy transfer.

Overall, bioluminescence has arisen over 40 times in evolutionary history. In evolution, luciferins tend to vary little: one in particular, coelenterazine, is the light emitting pigment for nine phyla (groups of very different organisms), including polycystine radiolaria, Cercozoa (Phaeodaria), protozoa, comb jellies, cnidaria including jellyfish and corals, crustaceans, molluscs, arrow worms and vertebrates (ray-finned fish). Not all these organisms synthesise coelenterazine: some of them obtain it through their diet. Conversely, luciferase enzymes vary widely and tend to be different in each species.

Distribution

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Huge numbers of dinoflagellates creating bioluminescence in breaking waves

Bioluminescence occurs widely among animals, especially in the open sea, including fish, jellyfish, comb jellies, crustaceans, and cephalopod molluscs; in some fungi and bacteria; and in various terrestrial invertebrates including insects. In marine coastal habitats, about 2.5% of organisms are estimated to be bioluminescent, whereas in pelagic habitats in the eastern Pacific, about 76% of the main taxa of deep-sea animals have been found to be capable of producing light. More than 700 animal genera have been recorded with light-producing species. Most marine light-emission is in the blue and green light spectrum. However, some loose-jawed fish emit red and infrared light, and the genus Tomopteris emits yellow light.

The most frequently encountered bioluminescent organisms may be the dinoflagellates in the surface layers of the sea, which are responsible for the sparkling luminescence sometimes seen at night in disturbed water. At least 18 genera exhibit luminosity. Luminescent dinoflagellate ecosystems are present in warm water lagoons and bays with narrow openings to the ocean. A different effect is the thousands of square miles of the ocean which shine with the light produced by bioluminescent bacteria, known as mareel or the milky seas effect.

Pelagic zone

Bioluminescence is abundant in the pelagic zone, with the most concentration at depths devoid of light and surface waters at night. These organisms participate in diurnal vertical migration from the dark depths to the surface at night, dispersing the population of bioluminescent organisms across the pelagic water column. The dispersal of bioluminescence across different depths in the pelagic zone has been attributed to the selection pressures imposed by predation and the lack of places to hide in the open sea. In depths where sunlight never penetrates, often below 200m, the significance of bioluminescent is evident in the retainment of functional eyes for organisms to detect bioluminescence.

Bacterial symbioses

Organisms often produce bioluminescence themselves, rarely do they generate it from outside phenomena. However, there are occasions where bioluminescence is produced by bacterial symbionts that have a symbiotic relationship with the host organism. Although many luminous bacteria in the marine environment are free-living, a majority are found in symbiotic relationships that involve fish, squids, crustaceans etc. as hosts. Most luminous bacterial inhabit the marine sea, with Photobacterium and Vibrio genera dominating the marine environment.

In the symbiotic relationship, bacterium benefit from having a source of nourishment and a refuge to grow. Hosts obtain these bacterial symbionts either from the environment, spawning, or the luminous bacterium is evolving with their host. Coevolutionary interactions are suggested as host organisms’ anatomical adaptations have become specific to only certain luminous bacteria, to suffice ecological dependence of bioluminescence.

Benthic zone

Bioluminescence is widely studied amongst species located in the mesopelagic zone, but the benthic zone at mesopelagic depths has remained widely unknown. Benthic habitats at depths beyond the mesopelagic are also poorly understood due to the same constraints. Unlike the pelagic zone where the emission of light is undisturbed in the open sea, the occurrence of bioluminescence in the benthic zone is less common. It has been attributed to the blockage of emitted light by a number of sources such as the sea floor, and inorganic and organic structures. Visual signals and communication that is prevalent in the pelagic zone such as counterillumination may not be functional or relevant in the benthic realm. Bioluminescence in bathyal benthic species still remains poorly studied due to difficulties of the collection of species at these depths.

Uses in nature

Bioluminescence has several functions in different taxa. Steven Haddock et al. (2010) list as more or less definite functions in marine organisms the following: defensive functions of startle, counterillumination (camouflage), misdirection (smoke screen), distractive body parts, burglar alarm (making predators easier for higher predators to see), and warning to deter settlers; offensive functions of lure, stun or confuse prey, illuminate prey, and mate attraction/recognition. It is much easier for researchers to detect that a species is able to produce light than to analyze the chemical mechanisms or to prove what function the light serves. In some cases the function is unknown, as with species in three families of earthworm (Oligochaeta), such as Diplocardia longa where the coelomic fluid produces light when the animal moves. The following functions are reasonably well established in the named organisms.

Counterillumination camouflage

In many animals of the deep sea, including several squid species, bacterial bioluminescence is used for camouflage by counterillumination, in which the animal matches the overhead environmental light as seen from below. In these animals, photoreceptors control the illumination to match the brightness of the background. These light organs are usually separate from the tissue containing the bioluminescent bacteria. However, in one species, Euprymna scolopes, the bacteria are an integral component of the animal's light organ.

Attraction

*Stauroteuthis syrtensis* bioluminescent photophores

Bioluminescence is used in a variety of ways and for different purposes. The cirrate octopod Stauroteuthis syrtensis uses emits bioluminescence from its sucker like structures. These structures are believed to have evolved from what are more commonly known as octopus suckers. They do not have the same function as the normal suckers because they no longer have any handling or grappling ability due its evolution of photophores. The placement of the photophores are within the animals oral reach, which leads researchers to suggest that it uses it bioluminescence to capture and lure prey.

Fireflies use light to attract mates. Two systems are involved according to species; in one, females emit light from their abdomens to attract males; in the other, flying males emit signals to which the sometimes sedentary females respond. Click beetles emit an orange light from the abdomen when flying and a green light from the thorax when they are disturbed or moving about on the ground. The former is probably a sexual attractant but the latter may be defensive. Larvae of the click beetle Pyrophorus nyctophanus live in the surface layers of termite mounds in Brazil. They light up the mounds by emitting a bright greenish glow which attracts the flying insects on which they feed.

In the marine environment, use of luminescence for mate attraction is chiefly known among ostracods, small shrimplike crustaceans, especially in the family Cyprididae. Pheromones may be used for long-distance communication, with bioluminescence used at close range to enable mates to "home in". A polychaete worm, the Bermuda fireworm creates a brief display, a few nights after the full moon, when the female lights up to attract males.

Defense

The defense mechanisms for bioluminescent organisms can come in multiple forms; startling prey, counterillumination, smoke screen or misdirection, distractive body parts, burglar alarm, sacrificial tag or warning coloration. The shrimp family Oplophoridae Dana use their bioluminescence as a way of startling the predator that is after them. Acanthephyra purpurea, within the Oplophoridae family, uses its photophores to emit light, and can secrete a bioluminescent substance when in the presence of a predator. This secretory mechanism is common among prey fish.

Many cephalopods, including at least 70 genera of squid, are bioluminescent. Some squid and small crustaceans use bioluminescent chemical mixtures or bacterial slurries in the same way as many squid use ink. A cloud of luminescent material is expelled, distracting or repelling a potential predator, while the animal escapes to safety. The deep sea squid Octopoteuthis deletron may autotomise portions of its arms which are luminous and continue to twitch and flash, thus distracting a predator while the animal flees.

Dinoflagellates may use bioluminescence for defense against predators. They shine when they detect a predator, possibly making the predator itself more vulnerable by attracting the attention of predators from higher trophic levels. Grazing copepods release any phytoplankton cells that flash, unharmed; if they were eaten they would make the copepods glow, attracting predators, so the phytoplankton's bioluminescence is defensive. The problem of shining stomach contents is solved (and the explanation corroborated) in predatory deep-sea fishes: their stomachs have a black lining able to keep the light from any bioluminescent fish prey which they have swallowed from attracting larger predators.

The sea-firefly is a small crustacean living in sediment. At rest it emits a dull glow but when disturbed it darts away leaving a cloud of shimmering blue light to confuse the predator. During World War II it was gathered and dried for use by the Japanese army as a source of light during clandestine operations.

The larvae of railroad worms (Phrixothrix) have paired photic organs on each body segment, able to glow with green light; these are thought to have a defensive purpose. They also have organs on the head which produce red light; they are the only terrestrial organisms to emit light of this color.

Warning

Aposematism is a widely used function of bioluminescence, providing a warning that the creature concerned is unpalatable. It is suggested that many firefly larvae glow to repel predators; some millipedes glow for the same purpose. Some marine organisms are believed to emit light for a similar reason. These include scale worms, jellyfish and brittle stars but further research is needed to fully establish the function of the luminescence. Such a mechanism would be of particular advantage to soft-bodied cnidarians if they were able to deter predation in this way. The limpet Latia neritoides is the only known freshwater gastropod that emits light. It produces greenish luminescent mucus which may have an anti-predator function. The marine snail Hinea brasiliana uses flashes of light, probably to deter predators. The blue-green light is emitted through the translucent shell, which functions as an efficient diffuser of light.

Communication

Communication in the form of quorum sensing plays a role in the regulation of luminescence in many species of bacteria. Small extracellularly secreted molecules stimulate the bacteria to turn on genes for light production when cell density, measured by concentration of the secreted molecules, is high.

Pyrosomes are colonial tunicates and each zooid has a pair of luminescent organs on either side of the inlet siphon. When stimulated by light, these turn on and off, causing rhythmic flashing. No neural pathway runs between the zooids, but each responds to the light produced by other individuals, and even to light from other nearby colonies. Communication by light emission between the zooids enables coordination of colony effort, for example in swimming where each zooid provides part of the propulsive force.

Some bioluminous bacteria infect nematodes that parasitize Lepidoptera larvae. When these caterpillars die, their luminosity may attract predators to the dead insect thus assisting in the dispersal of both bacteria and nematodes. A similar reason may account for the many species of fungi that emit light. Species in the genera Armillaria, Mycena, Omphalotus, Panellus, Pleurotus and others do this, emitting usually greenish light from the mycelium, cap and gills. This may attract night-flying insects and aid in spore dispersal, but other functions may also be involved.

Quantula striata is the only known bioluminescent terrestrial mollusc. Pulses of light are emitted from a gland near the front of the foot and may have a communicative function, although the adaptive significance is not fully understood.

Mimicry

A deep sea anglerfish, *Bufoceratias wedli*, showing the esca (lure)

Bioluminescence is used by a variety of animals to mimic other species. Many species of deep sea fish such as the anglerfish and dragonfish make use of aggressive mimicry to attract prey. They have an appendage on their heads called an esca that contains bioluminescent bacteria able to produce a long-lasting glow which the fish can control. The glowing esca is dangled or waved about to lure small animals to within striking distance of the fish.

The cookiecutter shark uses bioluminescence to camouflage its underside by counterillumination, but a small patch near its pectoral fins remains dark, appearing as a small fish to large predatory fish like tuna and mackerel swimming beneath it. When such fish approach the lure, they are bitten by the shark.

Female Photuris fireflies sometimes mimic the light pattern of another firefly, Photinus, to attract its males as prey. In this way they obtain both food and the defensive chemicals named lucibufagins, which Photuris cannot synthesize.

South American giant cockroaches of the genus Lucihormetica were believed to be the first known example of defensive mimicry, emitting light in imitation of bioluminescent, poisonous click beetles. However, doubt has been cast on this assertion, and there is no conclusive evidence that the cockroaches are bioluminescent.

Illumination

While most marine bioluminescence is green to blue, some deep sea barbeled dragonfishes in the genera Aristostomias, Pachystomias and Malacosteus emit a red glow. This adaptation allows the fish to see red-pigmented prey, which are normally invisible to other organisms in the deep ocean environment where red light has been filtered out by the water column. The fish is able to utilize the longer wavelength to act as a spotlight for its prey that only it is able to see. In addition to the utilization of the light for predation, it has been hypothesized that the fish use this to communicate with each other to find potential mates. The ability of the fish to see this light is explained by the presence of specialized rhodopsin pigment. The angler siphonophore (Erenna), also utilizes red bioluminescence in appendages to lure fish.

The mechanism of light creation is through a suborbital photophore that utilizes gland cells which produce exergonic chemical reactions that produce light with a longer, red wavelength. The dragonfish species which produce the red light also produce blue light in photophore on the dorsal area. The main function of this is to alert the fish to the presence of its prey. The additional pigment is thought to be assimilated from chlorophyll derivatives found in the copepods which form part of its diet.

Biotechnology

Biology and medicine

Bioluminescent organisms are a target for many areas of research. Luciferase systems are widely used in genetic engineering as reporter genes, each producing a different color by fluorescence, and for biomedical research using bioluminescence imaging. For example, the firefly luciferase gene was used as early as 1986 for research using transgenic tobacco plants. Vibrio bacteria symbiose with marine invertebrates such as the Hawaiian bobtail squid (Euprymna scolopes), are key experimental models for bioluminescence. Bioluminescent activated destruction is an experimental cancer treatment.

In Vivo luminescence cell and animal imaging uses dyes and fluorescent proteins as chromophores. The characteristics of each chromophore determine which cell area(s) will be targeted and illuminated.

Light production

The structures of photophores, the light producing organs in bioluminescent organisms, are being investigated by industrial designers. Engineered bioluminescence could perhaps one day be used to reduce the need for street lighting, or for decorative purposes if it becomes possible to produce light that is both bright enough and can be sustained for long periods at a workable price.The gene that makes the tails of fireflies glow has been added to mustard plants. The plants glow faintly for an hour when touched, but a sensitive camera is needed to see the glow. University of Wisconsin–Madison is researching the use of genetically engineered bioluminescent E. coli bacteria, for use as bioluminescent bacteria in a light bulb. In 2011, Philips launched a microbial system for ambience lighting in the home. An iGEM team from Cambridge (England) has started to address the problem that luciferin is consumed in the light-producing reaction by developing a genetic biotechnology part that codes for a luciferin regenerating enzyme from the North American firefly. In 2016, Glowee, a French company started selling bioluminescent lights for shop fronts and street signs, for use between 1 and 7 in the morning when the law forbids use of electricity for this purpose. They used the bioluminescent bacterium Aliivibrio fischeri, but the maximum lifetime of their product was three days. In April 2020, plants were genetically engineered to glow more brightly using genes from the bioluminescent mushroom Neonothopanus nambi to convert caffeic acid into luciferin.

ATP bioluminescence

ATP bioluminescence is the process in which ATP is used to generate luminescence in an organism. It proves to be a very good biosensor to test cell viability. Optical biosensors include process of measurement of luminescence, fluorescence absorbance or emission. Through these measurements, quantitative measurement of ATP bioluminescence is applied to detect existence of living microbes only. Since the method is quick and convenient, it results in real-time data. It is faster, economical and easier to work with. Optical biosensors sense the observed optical signal based on measuring the photons involved in the phenomenon (spiking) It depends on the interaction of microbes with analytes. Thus, it is correlated with the concentration of the microbial population which is determined through this method.

Differentiation between living and non living cells

In ATP bioluminescence, it is assumed that all living cells in the same have the same amount of ATP over time during the chemical reaction between luciferin, luciferase to produce ATP, This is done in order to measure the viability of the cell and allows the researcher to measure the amount of living and dead cells in the sample on basis of presence or absence of ATP. Living cells that contain ATP produce a bioluminescent flash due to the luciferin-luciferase reaction in presence of ATP. Dead cells do not produce any bioluminescence due to absence of ATP The amount of the intensity of the signal is constant for each living cell in a healthy sample. In this way, the overall number of living cells within a sample is determined.

Process of measurement of microbial population

ATP, which is a fundamental compound in the luciferase reaction, is utilized and in the second step, oxyluciferin is produced. The oxyluciferin is produced in an excited state, which produces light when it goes back to ground state. The light emitted is detected by a luminometer. Concentration of the ATP is directly proportional to the expressed light measured as Relative Light Units (RLU). A receiver operating characteristic (ROC) is used to calculate the sensitivity and specificity of the measurements. There is direct correlation between luminescence intensity and concentration of standard ATP. There is a direct correlation between bioluminescence and colony forming unit (CFU). Thus, concentration of standard ATP and CFU gives a standard correlation. In this way, ATP is measured and microbial population is determined through bioluminescence.

However, it is important to keep in mind that different types of microbial populations are determined through different sets of ATP assays using other substrates and reagents. Renilla and Gaussia based cell viability assays use the substrate coelenterazine.

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