Calcification in changing oceans

What do mollusks, starfish, and corals have in common? Aside from their shared marine habitat, they are all calcifiers — organisms that use calcium from their environment to create hard carbonate skeletons and shells for stability and protection.The June issue of the Biological Bulletin, published by the Marine Biological Laboratory, addresses the challenges faced by these species as ocean composition changes worldwide.As atmospheric carbon dioxide rises, the world’s oceans are becoming warmer and more acidic. This impact of global climate change threatens the survival of calcifying species because of the reduced saturation of the carbonate minerals required for calcification.The ability to calcify arose independently in many species during the Cambrian era, when calcium levels in seawater increased. This use of calcium carbonate promoted biodiversity, including the vast array of calcifiers seen today.”Today, modern calcifiers face a new and rapidly escalating crisis caused by warming and acidification of the oceans with a reduction in availability of carbonate minerals, a change driven by the increase in atmospheric CO2 due to anthropogenic emissions and industrialization. The CO2 itself can also directly cause metabolic stress,” write the issue’s co-editors, Maria Byrne of the University of Sydney; and Gretchen Hofmann of the University of California-Santa Barbara.Contributors to the journal address this timely issue across many taxa and from a variety of perspectives, from genomic to ecosystem-wide.Janice Lough and Neal Cantin of the Australian Institute of Marine Science review historical data on coral reefs to look at potential environmental stressors, while Philippe Dubois (Universit Libre de Bruxelles) discusses sea urchin skeletons.Other researchers address lesser-known organisms that are nevertheless critical to marine ecosystems. Abigail Smith of the University of Otago examines how bryozoans, a group of aquatic invertebrate filter-feeders, increase biodiversity by creating niche habitats, and what features make them particularly sensitive to calcium fluctuations.Evans and Watson-Wynn (California State University-East Bay) take a molecular approach in a meta-analysis showing that ocean acidification is effecting genetic changes in sea urchin larvae. Several papers take a broader population-based view by studying the effect of ocean acidification on predator-prey interactions in mollusks (Kroeker and colleagues of the University of California-Davis) and oysters (Wright and colleagues of the University of Western Sydney).”The contributors have identified key knowledge gaps in the fast evolving field of marine global change biology and have provided many important insights,” the co-editors write.By sharing research on this topic from researchers around the world, the Biological Bulletin is raising awareness of some of the greatest threats to the oceans today and emphasizing the global nature of the problem.Story Source:The above story is based on materials provided by The Marine Biological Laboratory. The original article was written by Gina Hebert. Note: Materials may be edited for content and length.

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Pathways that direct immune system to turn ‘on’ or ‘off’ found

A key discovery explaining how components of the immune system determine whether to activate or to suppress the immune system, made by Kelvin Lee, MD, Professor of Oncology and Co-Leader of the Tumor Immunology and Immunotherapy Program at Roswell Park Cancer Institute (RPCI), and colleagues led to published findings being selected as the “Paper of the Week” by the Journal of Biological Chemistry (JBC). The honor places his work among the top 2 percent — in terms of significance and overall importance — of the year’s manuscripts reviewed by the journal.This research focused on the immune system’s dendritic cells (DCs), crucial cells that initiate and regulate immune responses. For example, the dendritic cells activate T lymphocytes to fight an infection or cancer. Curiously, they are also known to suppress the immune response. Determining when DCs turn the immune response “on” or “off” is a major question in immunology.For this project, Dr. Lee’s team explored two receptors (called CD80 and CD86) expressed on the surface of dendritic cells that trigger the cells to make either immune-stimulating factors (interleukin-6) or immune-suppressive factors (indolemine 2, 3 dioxygenase, IDO). They defined the intracellular pathways by which the receptors triggered each response and also uncovered a previously unrecognized interaction with another receptor called Notch-1.Understanding how these pathways are put together opens the door to targeting components of the pathway so physicians can manipulate the dendritic cells to either activate or suppress the immune system in a way that’s therapeutically beneficial.“Activating the immune response would enhance a patient’s response to a vaccine designed to prevent a cancer from growing or recurring,” explains Dr. Lee. “Suppressing or blocking an unwanted immune response would be helpful in organ-transplant cases, to prevent rejection, or in autoimmune diseases like lupus and rheumatoid arthritis.”With regard to cancer, Dr. Lee explains how manipulating the CD80/CD86 pathway could impact treatment for multiple myeloma, a cancer of a type of white blood cell in the bone marrow.“Myeloma cells use this pathway to survive and grow by inducing the DC to make IL-6 — which promotes the cancer cells’ survival — and IDO, which blocks anti-cancer responses,” he says. …

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Plants convert energy at lightning speed

A new way of measuring how much light a plant can tolerate could be useful in growing crops resilient to a changing climate, according to scientists from Queen Mary University of London.”This is the first time we have been able to quantify a plant’s ability to protect itself against high light intensity,” said Professor Alexander Ruban, co-author of the study and Head of the Cell and Molecular Biology Division at Queen Mary’s School of Biological and Chemical Science.Professor Ruban added: “A changing climate will lead to fluctuations in temperature, humidity, drought and light. Knowing the limits of how much sunlight a crop can happily tolerate could be valuable information for farmers or people who breed new plants.”Publishing in the journal Philosophical Transactions of the Royal Society B today (Monday 3 March) the scientists demonstrate a novel method that enables them to relate the photoprotective capacity of a plant to the intensity of environmental light by measuring the fluorescence of the pigment chlorophyll, which is responsible for absorbing sunlight.Co-author Erica Belgio, also at Queen Mary’s School of Biological and Chemical Science said: “The plants we used to measure the light varied in their capacity to protect themselves against high levels of intensity. We exposed them to gradually increasing levels of light, from the sunlight more common on a rainy day to the light you would find at noon on summer’s day in the south of France and recorded the responses.”The researchers found the plants grown without the ability to respond quickly to high light intensity had a reduced capacity to protect themselves from damage.”The photosynthetic apparatus in the plants is like the retina in human eyes — it is sensitive to how much light can be soaked up,” commented Professor Ruban.Story Source:The above story is based on materials provided by Queen Mary, University of London. Note: Materials may be edited for content and length.

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How gut bacteria communicate within our bodies, build special relationship

Communication is vital to any successful relationship. Researchers from the Institute of Food Research and the University of East Anglia have discovered how the beneficial bacteria in our guts communicate with our own cells.This is a key step in understanding how our bodies maintain a close relationship with the population of gut bacteria that plays crucial roles in maintaining our health, fighting infection and digesting our food.A study, published in the journal Cell Reports, shows that the gut bacteria produce an enzyme that modifies signalling in cells lining the gut. The enzyme also has another role in breaking down food components.”Our study provides a breakthrough in understanding how bacteria communicate across different kingdoms to influence our own cells’ behavior, as well as how we digest our food,” said Dr Regis Stentz from the IFR, which is strategically funded by the Biotechnology and Biological Sciences Research Council.We all rely on trillions of bacteria in our gut to break down certain components of our diet. One example is phytate, the form phosphorus takes in cereals and vegetables. Broken down phytate is a source of vital nutrients, but in its undigested form it has detrimental properties. It binds to important minerals preventing them being taken up by the body, causing conditions like anemia, especially in developing countries. Phytate also leads to excess phosphorus leaching into the soil from farm animal waste, and feed supplements are used to minimize this.But despite the importance of phytate, we know very little about how it is broken down in our gut. To address this Dr Stentz and colleagues screened the genomes of hundreds of different species of gut bacteria. They found, in one of the most prominent gut bacteria species, an enzyme able to break down phytate. In collaboration with Norwich Research Park colleagues at the University of East Anglia, they crystallized this enzyme and solved its 3D structure. …

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Complex relationship between phosphorus levels, nitrogen removal in lakes

Oct. 10, 2013 — In the land of 10,000 lakes, one lake has been the starting place for research with implications for big lakes around the world. According to a study published online this week in Science, University of Minnesota researchers, building from studies of nitrogen levels in Lake Superior, uncovered a good news/bad news scenario for lake health that has long-term, global implications for pollution control efforts.While many water-quality cleanup efforts focusing on the reduction of phosphorus have been highly effective, that success can also result in a decrease in microbial processes that remove nitrogen from water. Nitrogen accumulation in large lakes can lead to nitrogen pollution downstream, in rivers and coastal areas. The findings suggest that human-caused acceleration of global nitrogen and phosphorus cycles have boosted nitrogen removal processes in small to medium-size lakes. But in many of Earth’s large lakes, these effects are reduced by successful control of phosphorus, resulting in nitrogen accumulation.”Freshwater ecosystems, including lakes, streams and wetlands, are a large global sink for reactive nitrogen,” says lead author Jacques Finlay, an associate professor in the College of Biological Sciences (CBS). “By reducing one aquatic pollutant — phosphorus — we are in some cases reducing the ability of lakes to remove nitrogen.” Gaston Small, an assistant professor at the University of St. Thomas, and Robert Sterner, a fellow CBS ecology professor, co-authored the study.To assess the influence of phosphorus on nitrogen removal, the researchers used a comparative approach — they examined the differences between how much nitrogen goes into lakes and how much comes out downstream — coupled with time-series analyses of nitrogen and phosphorus concentration in large lakes.”The work was motivated by our thinking about the case of a single lake — Lake Superior. This lake is one that we would expect to efficiently remove nitrogen, but it doesn’t, and it has extremely low phosphorus, so this work arose from efforts to generalize beyond a single system,” Finlay says.The excess nutrients can come from a variety of sources. City dwellers contribute nitrogen through sewage, lawn fertilizer, vehicle exhaust and pets. …

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New evidence that orangutans and gorillas can match images based on biological categories

Sep. 10, 2013 — The ability to form a general concept that connects what we know about the members of a category allows humans to respond appropriately when they encounter a novel member of that category. At an early age, children form categories to, for example, differentiate animals from inanimate objects and to differentiate dogs from cats. New research shows that other apes may form similar categories to represent different types of animals.There are at least two ways to visually identify an animal as being similar to any other: the animals may be within a species and therefore closely resemble each other (so called ‘perceptual’ differences) or the animals may be considered to meet the criteria for a broader mental concept (for example, “reptiles do not have fur, they have short legs or have no legs, and lay eggs — these all seem like reptiles”). Concept formation in human children has been subjected to extensive experimental study, with much focus on the interplay between concept acquisition and language acquisition. It has been proposed that these broader concepts depend upon formal scientific training and/or the ability to form verbal labels for such concepts. If non-human animals represent such concepts, this finding would be evidence against such a view. It is surprising then that the existence of natural categories, such as classification of animals, has not been extensively studied in language-less non-human apes. Studies of concepts in animals have instead paid close attention to the perceptual features that are used by the animals to extract information about category membership but have not typically allowed animals to demonstrate that they can also form concepts at different levels of breadth simultaneously.In this study, a young female gorilla and four orangutans of various ages were shown images of animals and asked to match them to an image from the same species or family (i.e. one with a perceptual similarity). …

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What is the brain telling us about the diagnoses of schizophrenia?

Sep. 5, 2013 — We live in the most exciting and unsettling period in the history of psychiatry since Freud started talking about sex in public.On the one hand, the American Psychiatric Association has introduced the fifth iteration of the psychiatric diagnostic manual, DSM-V, representing the current best effort of the brightest clinical minds in psychiatry to categorize the enormously complex pattern of human emotional, cognitive, and behavioral problems. On the other hand, in new and profound ways, neuroscience and genetics research in psychiatry are yielding insights that challenge the traditional diagnostic schema that have long been at the core of the field.”Our current diagnostic system, DSM-V represents a very reasonable attempt to classify patients by their symptoms. Symptoms are an extremely important part of all medical diagnoses, but imagine how limited we would be if we categorized all forms of pneumonia as ‘coughing disease,” commented Dr. John Krystal, Editor of Biological Psychiatry.A paper by Sabin Khadka and colleagues that appears in the September 15th issue of Biological Psychiatry advances the discussion of one of these roiling psychiatric diagnostic dilemmas.One of the core hypotheses is that schizophrenia and bipolar disorder are distinct scientific entities. Emil Kraepelin, credited by many as the father of modern scientific psychiatry, was the first to draw a distinction between dementia praecox (schizophrenia) and manic depression (bipolar disorder) in the late 19th century based on the behavioral profiles of these syndromes. Yet, patients within each diagnosis can have a wide variation of symptoms, some symptoms appear to be in common across these diagnoses, and antipsychotic medications used to treat schizophrenia are very commonly prescribed to patients with bipolar disorder.But at the level of brain circuit function, do schizophrenia and bipolar differ primarily by degree or are there clear categorical differences? To answer this question, researchers from a large collaborative project called BSNIP looked at a large sample of patients diagnosed with schizophrenia or bipolar disorder, their healthy relatives, and healthy people without a family history of psychiatric disorder.They used a specialized analysis technique to evaluate the data from their multi-site study, which revealed abnormalities within seven different brain networks. Generally speaking, they found that schizophrenia and bipolar disorder showed similar disturbances in cortical circuit function. When differences emerged between these two disorders, it was usually because schizophrenia appeared to be a more severe disease. …

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Unprecedented control of genome editing in flies promises insight into human development, disease

Aug. 23, 2013 — In an era of widespread genetic sequencing, the ability to edit and alter an organism’s DNA is a powerful way to explore the information within and how it guides biological function.A paper from the University of Wisconsin-Madison in the August issue of the journal Genetics takes genome editing to a new level in fruit flies, demonstrating a remarkable level of fine control and, importantly, the transmission of those engineered genetic changes across generations.Both features are key for driving the utility and spread of an approach that promises to give researchers new insights into the basic workings of biological systems, including embryonic development, nervous system function, and the understanding of human disease.”Genome engineering allows you to change gene function in a very targeted way, so you can probe function at a level of detail” that wasn’t previously possible, says Melissa Harrison, an assistant professor of biomolecular chemistry in the UW-Madison School of Medicine and Public Health and one of the three senior authors of the new study.Disrupting individual genes has long been used as a way to study their roles in biological function and disease. The new approach, based on molecules that drive a type of bacterial immune response, provides a technical advance that allows scientists to readily engineer genetic sequences in very detailed ways, including adding or removing short bits of DNA in chosen locations, introducing specific mutations, adding trackable tags, or changing the sequences that regulate when or where a gene is active.The approach used in the new study, called the CRISPR RNA/Cas9 system, has developed unusually fast. First reported just one year ago by scientists at the Howard Hughes Medical Institute and University of California, Berkeley, it has already been applied to most traditional biological model systems, including yeast, zebrafish, mice, the nematode C. elegans, and human cells. The Wisconsin paper was the first to describe it in fruit flies and to show that the resulting genetic changes could be passed from one generation to the next.”There was a need in the community to have a technique that you could use to generate targeted mutations,” says Jill Wildonger, a UW-Madison assistant professor of biochemistry and another senior author of the paper. “The need was there and this was the technical advance that everyone had been waiting for.””The reason this has progressed so quickly is that many researchers — us included — were working on other, more complicated, approaches to do exactly the same thing when this came out,” adds genetics assistant professor Kate O’Connor-Giles, the third senior author. “This is invaluable for anyone wanting to study gene function in any organism and it is also likely to be transferable to the clinical realm and gene therapy.”The CRISPR RNA/Cas9 system directs a DNA-clipping enzyme called Cas9 to snip the DNA at a targeted sequence. This cut then stimulates the cell’s existing DNA repair machinery to fill in the break while integrating the desired genetic tweaks. The process can be tailored to edit down to the level of a single base pair — the rough equivalent of changing a single letter in a document with a word processor.The broad applicability of the system is aided by a relatively simple design that can be customized through creation of a short RNA sequence to target a specific sequence in the genome to generate the desired changes. …

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Elevated levels of copper in amyloid plaques associated with neurodegeneration in mouse models of Alzheimer’s disease

Aug. 21, 2013 — Metals such as iron, copper, and zinc are important for many biological processes. In recent years, studies have shown that these nutritionally-essential metals are elevated in human Alzheimer’s disease (AD) brains and some animal models of AD. Scientists are now exploring whether these metals are causing the neurodegeneration seen in AD or are indicative of other ongoing pathologic processes.In a new study, investigators used synchrotron x-ray fluorescence microscopy to image metal ions in the brain, focusing on the amyloid plaques that are the hallmark of AD. They found that, in two AD mouse models that exhibit neurodegeneration, the plaques contained about 25% more copper than an AD mouse model that shows little neurodegeneration. Looking at other metals, they found that none of the mouse models had significant increases in iron and very little increases in zinc. Metal content was not related to the age of the plaque. The study is reported in the current issue of Biomedical Spectroscopy and Imaging.”Since excess copper should not be ‘free’ in the brain to bind to the plaques, these data suggest that the cellular control of copper is altered in AD, which may lead to toxic reactions between free copper ions and neurons,” comments lead investigator Lisa M. Miller, PhD, a biophysical chemist in the Photon Sciences Directorate at Brookhaven National Laboratory. In previous work, Dr. …

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Playing video games can boost brain power

Aug. 21, 2013 — Certain types of video games can help to train the brain to become more agile and improve strategic thinking, according to scientists from Queen Mary University of London and University College London (UCL).The researchers recruited 72 volunteers and measured their ‘cognitive flexibility’ described as a person’s ability to adapt and switch between tasks, and think about multiple ideas at a given time to solve problems.Two groups of volunteers were trained to play different versions of a real-time strategy game called StarCraft, a fast-paced game where players have to construct and organise armies to battle an enemy. A third of the group played a life simulation video game called The Sims, which does not require much memory or many tactics.All the volunteers played the video games for 40 hours over six to eight weeks, and were subjected to a variety of psychological tests before and after. All the participants happened to be female as the study was unable to recruit a sufficient number of male volunteers who played video games for less than two hours a week.The researchers discovered that those who played StarCraft were quicker and more accurate in performing cognitive flexibility tasks, than those who played The Sims.Dr Brian Glass from Queen Mary’s School of Biological and Chemical Sciences, said: “Previous research has demonstrated that action video games, such as Halo, can speed up decision making but the current work finds that real-time strategy games can promote our ability to think on the fly and learn from past mistakes.””Our paper shows that cognitive flexibility, a cornerstone of human intelligence, is not a static trait but can be trained and improved using fun learning tools like gaming.”Professor Brad Love from UCL, said: “Cognitive flexibility varies across people and at different ages. For example, a fictional character like Sherlock Holmes has the ability to simultaneously engage in multiple aspects of thought and mentally shift in response to changing goals and environmental conditions.””Creative problem solving and ‘thinking outside the box’ require cognitive flexibility. Perhaps in contrast to the repetitive nature of work in past centuries, the modern knowledge economy places a premium on cognitive flexibility.”Dr Glass added: “The volunteers who played the most complex version of the video game performed the best in the post-game psychological tests. We need to understand now what exactly about these games is leading to these changes, and whether these cognitive boosts are permanent or if they dwindle over time. Once we have that understanding, it could become possible to develop clinical interventions for symptoms related to attention deficit hyperactivity disorder or traumatic brain injuries, for example.”

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A cautionary note on oxytocin as a treatment for psychiatric disorders

Aug. 12, 2013 — The hormone oxytocin is known for its widespread effects on social and reproductive processes, and recent data from intranasal administration in humans has produced hope for its use as a therapeutic in autism, schizophrenia, and other disorders.However, this leap to human use is happening without previous animal studies of long-term oxytocin administration, and without knowledge of the neurobiological mechanisms involved in the behavioral findings.A new study now published in Biological Psychiatry indicates that the promising short-term effects often observed after a single dose of oxytocin may not translate to positive effects after long-term administration.This research was led by Dr. Karen Bales, Professor and Vice Chair of Psychology at the University of California. She and her colleagues examined the long-term effects of oxytocin treatment using the prairie vole, a small rodent that forms strong life-long pair bonds and is thus often used in studies of social behavior.Both male and female voles were treated with one of three dosages of intranasal oxytocin, administered daily from weaning through sexual maturity. During this time, the researchers observed and recorded the voles’ social interactions. They also conducted tests of social and anxiety-related behaviors in the adult voles, after the oxytocin treatment had finished, allowing them to measure any long-term effects.As expected, oxytocin treatment increased social behavior in male voles, similar to the effects repeatedly observed in humans. However, the long-term effects were concerning, with male voles showing deficits in their typical behaviors.”In this study, we showed that long-term exposure to oxytocin in adolescent male prairie voles led to disruption of social bond formation in these males as adults,” explained Bales. “Male prairie voles which received a dose similar to that being tested in humans, or even a lower dose, did not form pair-bonds normally with their pair-mate. Instead these males chose to associate with a strange female.”This important finding should suggest caution in the long-term use of intranasal oxytocin in developing humans.”The fact that long term treatment with oxytocin had the opposite impact of initial doses with the same substance suggests that special strategies will be needed if oxytocin is ever to become a long-term treatment for autism or schizophrenia,” said Dr. John Krystal, Editor of Biological Psychiatry.Bales agrees, and added, “In our continuing research program, we also have preliminary data suggesting that these treatments caused long-term changes in the oxytocin system. …

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Moderate exercise could be good for your tendons, research shows

Aug. 7, 2013 — Moderate exercise could be good for keeping your tendons healthy according to new research from the University of East Anglia funded by Arthritis Research UK.The onset of tendon disease has previously been associated with exercise. However new research published n the journal Molecular Cell Research shows that doing moderate exercise could help guard against and treat the painful and often debilitating condition.The research team showed that moving around decreases a group of enzymes (metalloproteinases) that degrade tendon tissue and increase tendon protein.Tendon disease is caused by damage to a tendon at cellular level. Symptoms include chronic pain, inflammation, stiffness and reduced function.Lead researcher Dr Eleanor Jones, from UEA’s school of Biological Sciences, said: “The onset of tendon disease has always been associated with exercise, however this association has not been fully understood. We have shown that moderate exercise has a positive effect on tendons.”The team used human Achilles tendon cells which were seeded in rat tail collagen gels. These were then subjected to levels of strain experienced by human tendons to simulate moderate exercise.”In this study we talk about moderately high exercise and we would consider running to be moderately high. But it’s important to remember that our research was carried out in the lab so to confirm this we would need to complete further clinical studies.”The new findings also reveal how genes are regulated by the activation of the protein TGF-β (transforming growth factor beta). By investigating this pathway, researchers hope to find out more about how exercise is associated with tendon disease.

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Tahiti: A very hot biodiversity hot spot in the Pacific

Aug. 9, 2013 — A collaborative biological survey that focused on the insects of French Polynesia has resulted in the discovery of over 100 tiny predatory beetle species in Tahiti, 28 of these species newly described in the open-access journal ZooKeys.The predatory beetles range in size from 3-8 mm long, and have evolutionarily lost their flight wings, making them homebodies living in small patches of mountain forest. The author, James Liebherr of Cornell University, states “It is exhilarating working with such a fauna, because every new locality or ecological situation has the high probability of supporting a species nobody has seen before.”This adaptive radiation has evolved on an oceanic island less than 1.5 million years old, within an area of just over 1000 square kilometers. These beetles have diversified by speciating as fast as any animals worldwide, with each species estimated to last only 300,000 years before splitting into daughter species.Tahiti’s geological history has much to do with this evolutionary rate, as these beetles prefer to live in rain forests on high mountains that have become isolated through extensive erosion that has produced the broad, low-elevation river valleys so characteristic of the island. Yet some closely related species live on the same mountain ridge, just at different elevations or in different types of habitat.This level of specialization is what characterizes an adaptive radiation, where species exist within narrow ecological or geographic boundaries that mainland species would simply ignore or fly over. Yet this exuberant evolution may face a dark future, as invasive species from the mainland threaten the highly specialized island species. Predatory ants, such as the little fire ant, have invaded Tahiti, and have been recorded from some localities where native beetle species were collected by French entomologists in the 1970’s.”Now that the 101 species of small predatory beetles currently known from Tahiti can be identified, field sampling can be used to evaluate their conservation status relative to alien threats,” says Liebherr. Moreover he says, “Everybody who makes landfall on Tahiti, either by air or sea, should endeavor to disembark pest free so as to protect the many denizens of the mountain forests who make the native ecosystems work.”

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