Diagnosing diseases using a simple blood test

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Researchers from Qatar have developed biomarkers for plasma volume and red cell mass, which are used to monitor numerous disease states, such as heart failure, kidney disease or sepsis. The markers provide an applicable method to measure absolute plasma or red cell volumes, via a simple blood test, in a clinical set-up.

In their initial investigation, the scientists observed 33 healthy males over a period of six months. They collected monthly blood samples and concurrently estimated vascular volume.

They then analysed the individual variations of 45 common chemistry markers, such as total protein, cholesterol, calcium, transferrin, and albumin. These observed variations were then matched to the observed plasma volume variability. “We identified two panels of biomarkers, composed of 8 and 15 chemistry variables, which explained approximately 67% of plasma volume variance,” says corresponding author Louisa M. Lobigs, from Aspetar Sports Medicine Hospital, Doha, Qatar.

The scientist explains that, currently, vascular volumes are estimated in hospitals by calculating the change in concentration-based blood markers, such as hemoglobin concentration or hematocrit. This common approach produces relative values and assumes uniform mixing of the blood constituent (often not the case in the critically ill); it is also dependent on factors like the patient’s hydration levels, posture, their fluid intake. Alternatively, absolute vascular volumes can be estimated with radio-active tracers, but it’s a cumbersome and time-consuming approach, according to Lobigs.

The new method measures absolute volumes, and requires only a simple blood test.

“This is extremely promising news for improved volume management in the clinic,” she says. Validation of the model’s stability will be required before it can be streamlined among hospital patients.

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How changing sex helps “Nemo” survive and adapt

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Laura Casas, House of Wisdom guest blogger and King Abdullah University of Science & Technology (KAUST) marine biologist, talks to us about the orange salt water fish and how it used a marvelous evolutionary mechanism to conquer the seas.

Clownfish_AlFahal

Fran Saborido-Rey

How did a small, very bright, colorful fish that’s a poor swimmer become extensively distributed in tropical waters from the Indian to the western Pacific Oceans, including the Great Barrier Reef and the Red Sea?

Two processes have potentially played a role in the successful evolutionary adaptation of clownfishes: a mutual relationship with anemones – flower-like marine animals and relatives to corals – which provides shelter and protection in exchange for nourishment, plus their capacity to change sex when their partner dies, preventing the need for dangerous travel across the reef.

While the different aspects of this mutual relationship have been unveiled in dozens of studies, very little has been known about the mechanisms that orchestrate sex change in fishes.

Our new study at KAUST provides insights into the genetic mechanism governing social sex change in fish, using the Red Sea endemic species of clownfish, Amphiprion bicinctus, as a model in its natural habitat.

Clownfishes are monogamous, living in social assemblages as pairs or social groups consisting of a dominant female, always the largest in size, surrounded by her male partner and a variable number of immature juveniles of smaller size. They display a strong social hierarchy based on size; these hierarchies function as queues for breeding, so when a dominant female of a social group dies, all subordinates seize the opportunity to ascend in rank.

This way, the male is always poised to become female and rapidly changes sex to assume the vacated position, while the biggest juvenile rapidly matures into a male ensuring the ability to produce new generations without abandoning the anemone.

ClownfishExperiments_Credit_ThamerSHabis (3)

Thamer S. Habis

The confinement of an animal, however, is known to alter its normal behaviour but traditionally sex change has been studied using aquarium experiments. In our study, we localized sixteen families living on the exposed side of Al-Fahal reef, in the Central Red Sea and removed all the females to trigger the sex change process.

One sex-changing individual was sampled every five days for 1.5 months to cover the full time course of the sex change process and their transcriptional responses were assessed using RNA sequencing.

Our results show a response in the male´s brain which starts two weeks after the female’s disappearance and lasts for two additional weeks.

During this period, there is a marked down-regulation in deferentially expressed genes of sex-changing individuals, compared to mature males and females. We identify a large number of candidate genes, both well-known and novel potentially playing a role in sex change.

Based on our results, we propose a picture of the genetic mechanisms that take place during the sex shift: the aromatase gene known as cyp19a1 plays a central role by modulating the balance between estrogen and androgen signaling. Aromatase is involved in the production of estrogen.

The genes sox6 and foxp4 may play a role in regulating the expression of aromatase and/or other genes involved in steroid production at the brain level. The genes cyp19a1 and foxl2 play a pivotal role in the activation of the female pathway driving the sex gland transformation from testis to ovary during sex change, while Sox8, Dmrt1 and Amh are important for testis maintenance.

The results have not only provided important insight into the main genetic mechanism governing sex change and sex gland restructuring in hermaphrodite flowers or animals, but also detailed information on specific genes involved during every step of the process. Our study is the first genome-wide study in a social sex-changing species in its natural habitat and the dataset generated is a valuable genomic resource for a species with virtually no genetic information available in public datasets.

Future work would ideally explore whether the genetic processes underlying sex change in hermaphrodites is evolutionary conserved. We need to deepen our knowledge of the unexplored genetic mechanisms underlying such sex change.

As well, only a deep understanding of the genetic processes governing reproduction in hermaphrodites will allow us to anticipate how reproductive success might be affected by the temperature rise in coming years as a consequence of the climate change and give us a chance to conserve and protect the sea’s biodiversity.

Solar barques: Ritual vessels into the afterworld or real, functioning boats?

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Khufu solar boat museum, King Cheops ship in the museum at the base of the Great Pyramid, Giza, Cairo, Egypt.

Khufu solar boat museum, King Cheops ship in the museum at the base of the Great Pyramid, Giza, Cairo, Egypt.

Jack Sullivan / Alamy Stock Photo

The exact functions of the Khufu “solar vessels” unearthed south of the Pyramids of Giza, have come into question again after a new revelation by archaeologists showed that ancient Egyptians used metal in their boats.

The most famous of the vessels, and the largest, is the Khufu vessel, preserved in the Giza solar boat museum. The typically human-propelled vessels were discovered in several boat pits around the pyramids.

Now, a fresh dig near the Great Pyramid of Giza unearthed circular and U-shaped metal hooks in a piece of wood–eight metres in length, 40 centimetres­ wide–that belonged to the frame of a boat discovered during the same year as Khufu’s vessel.

In all the boats discovered from this era, “we have not found the use of metals in their frames like in this boat,” Mohamed Mostafa Abdel-Megeed, an antiquities ministry official and expert in boat-making in ancient Egypt, tells AFP.

In ancient Egypt, funerary boats were used to ferry the dead, most commonly in funeral processions of kings. The wooden boats were believed to be “magically charged” after having been used. And it’s the reason why ancient Egypt would dispose of them after use, since they were “dangerous to the living,” explains Pearce Paul Creasman, associate professor of Dendrochronology and Egyptian Archaeology and director of the Egyptian Expedition at the University of Arizona.

In the Old and Middle Kingdoms, funerary boats were buried near royal chambers at the pyramid complexes. Now, as far as many archaeologists believe, “solar boats were a concept, not necessarily a construction,” says the scientist, “to be used by the god Ra in his travels across the sky, perpetuating neheh, the cyclical nature of the world.” In iconography, solar barques feature a specific set of accouterments associated with them, setting them apart from other types of boats.

Creasman chats to Nature Middle East about the possible nature of the boats, in light of of the new discovery, the first of its kind.

NME: How significant is this discovery?

PPC: The discovery of metal used in association with the ships of ancient Egypt is significant as it fills a logical hole in our understanding. The Egyptians had metal and were capable seafarers, why wouldn’t they use the metals to improve the durability or function of their boats? Until the recent discoveries, including the Khufu II vessel as well as ship remains from the Red Sea harbor of Wadi Gawasis (dating to the Middle Kingdom), we lacked archaeological evidence to demonstrate such a link. While the finds from the Khufu II work have not yet been scientifically published, from the press photos it appears that the metal was used precisely where we might expect: at stress points, such as oarlocks. The totality of the importance of these finds will have to wait for the scientific publications and analyses, but this is a great start.

NME: Was not this seen before in ancient Egyptian boats?

PPC: In only one instance prior to the Khufu II finds has metal been found in association with the structure and function of ancient Egyptian boats, that is, the disarticulated boat parts from Wadi Gawasis. The Khufu II finds are, by far, the oldest and appear to be used in the locomotive aspects of the boat. While we have seen metal in association with sails and their ropes, we have not previously seen it in the human-propelled aspects of boats.

NME: Why is this an important piece of information for archaeologists?

PPC: In the more than 3,000 years of intensive maritime history for the pharaonic Egyptians, there must have been tens-of-thousands of boats created to traverse the waters. Yet, today we have comparatively little archaeological remains to understand the the ships that facilitated this maritime life: whole or part of only some 30 boats. So, any new clue in unraveling the mysteries of the world’s first great maritime society is extremely valuable.

Check Nature Middle East’s sister magazine For Science for the full coverage in Arabic.

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Empowering women scientists in MENA

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Funded by the Islamic Development Bank and the Bill & Melinda Gates Foundation, an international center for agriculture is promising to lay the ground work for a women empowerment initiative aimed at scientists, reportedly the first of its kind in the Middle East and North Africa (MENA) region.

The International Center for Biosaline Agriculture (ICBA) launched the design phase of the Young Arab Women Scientists Leadership Programme, dubbed Tamkeen (literally meaning empowerment in Arabic) this month.

Nature Middle East speaks to Setta Tutundjian, director of partnerships and knowledge management at ICBA, about the potential of this gender-specific science programme.

NME: How will your programme empower women involved in scientific research across the Middle East?

Setta Tutundjian: The objective of the Tamkeen program is to encourage young Arab women scientists to pursue a life-long career within the field of scientific research and development. The programme also aims to help women scientists interested in pursuing leadership positions to acquire the skills necessary to assume such leadership position within research institutes across the region.

The programme will develop  leadership and soft skills among participants in key areas such as negotiation, human resource management, science writing, proposal writing, planning, presentation, mentoring, deeper understanding of self-esteem and so on.

We expect this to be achieved through a careful mix of classroom training, online training, coaching and mentoring.

NME: You’re still designing the programme, correct?

ST: Yes. And a critical part of this phase includes conducting focus group discussions and interviews with young women scientists to fully understand the challenges and opportunities they currently face within their careers, as well as to hear from them on the elements of an ideal leadership program that can help them address some of the challenges they face. We want to build a program primarily based around their needs and aspirations.

NME: By identifying the barriers and challenges, do you mean that you plan to launch country-specific investigations into how women are faring in the research and development field?

ST: Besides focus group discussions and interviews with the women, the design phase will also include an assessment of current academic programmes on offer in the region and whether these programmes cater to leadership development among graduates. There will also be an assessment of regional and international capacity building programmes to leverage learning and best practices.

During the coming months, a gender expert, a leadership expert and an expert in training activities will gather to prepare modules and produce a detailed framework of the leadership programme incorporating the results of the various assessments.

NME: I can imagine that women in a country like Egypt would be facing starkly different challenges than, say, the women of the United Arab Emirates …

ST: We do have a unique understanding of the region and the differences that exist between the different countries, specifically when it comes to research and development. Our focus group sessions will be divided among three sub-regions (the Gulf, the Levant and North Africa) in order to cater to the differences among the regions and target countries.

NME: How do you plan to measure progress?

ST: Measuring short-term results will include references to quantity and quality of workshops, participant feedback, network reach and similar metrics. Measuring long-terms results and impact will consider the number of women leaders over time in research institutions in the region, and the increase in number of scientific publications of women scientists.

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Beating cancer with smarter use of radiation?

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This is a guest post by Nature Middle East writer Hebah Salama.

Cancers infect different tissues, and so they manifest differently, in various types, and require different treatments or sometimes a combination of treatments. Throw in variability among patients as a factor, and it’s even more complicated. It’s the reason why numerous studies are carried out every year to try and gauge the most effective therapy for different cancer types.

Now, researchers from Sudan and Lebanon specializing in medical physics and biochemistry have collaborated together on one such study. Their research deals with cancer cases in children, specifically analyzing the effect of different single radiation doses of X-rays on Rhabdomyosarcoma (RMS) – a malignant tumor involving skeletal muscle tissue.

Radiation, one of the most commonly used methods of cancer treatment, is known to cause damage in both healthy and cancerous tissue. It’s what sparked the known risk-benefit-ratio debate on whether the benefits from radiation therapy outweigh the harms. Scientists often discuss the different methods in which radiation can be used while keeping its side-effects to a minimum. As well, new technologies that provide high accuracy in dose delivery have been invented for this purpose; sparing healthy cells.

In this study, the scientists treated cultured RMS cells in vitro (outside of the human body) with therapeutic X-rays. The cells have shown to be resistant to radiation. Additionally, and depending on the radiation dosages, many of the treated cells have repaired from the X-rays’ radiation damage.

The scientists use this study to demonstrate that efforts put into studying tumors’ and healthy tissues’ biological responses to radiation based on tumor type should be stepped up. The more accurate the data provided about these types of responses, the better the outcome of patient treatment is.

“The advancement in technology should be met with more scientific research,” says Alexander Fadul lead researcher.

He adds that more patient oriented studies are certainly needed to determine the different parameters of radiation.

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Calgary Depression Scale for Schizophrenia, in Arabic

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Scientists from Qatar and the United States have managed to validate an Arabic version of the Calgary Depression Scale for Schizophrenia (CDSS) among patients with schizophrenia.

Schizophrenics commonly show both depressive and negative symptoms that can affect the prognosis and course of their treatment. Negative symptoms are disabling symptoms that have a major impact on the quality of life of patients, more so than positive symptoms, which are thought patterns and behaviors that patients acquire after they become ill.

Tests such as CDSS are designed to distinguish between depression, and negative symptoms that are distinctive of schizophrenia.

These tests are not diagnostic per se, “but they are mainly there to asses the severity of psychotic symptoms in schizophrenia and the possible associated depressive symptoms (using CDSS),” explains Hassen Al-Amin, professor of psychiatry at Weill Cornell Medicine-Qatar and corresponding author of the study that validated the psychiatric test.

“They are significant because they can help us know how sick these patients are and also to monitor how they are responding to treatment with time,” he says.

These types of tests have been used worldwide and their validity is established.

In order to make them work for Arab populations, experts and researchers had to translate the material thoroughly and decide the appropriate cultural equivalents in Arabic. “We then test the Arabic versions with Arab patients with schizophrenia and compare them with those obtained internationally to make sure that we have a valid scale that is culturally acceptable also,” says Al-Amin.

UAE’s green city grabs the attention of international researchers

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Masdar city, in the heart of the Gulf desert, on the outskirts of Abu Dhabi, has no light switches or water taps. In Masdar, movement sensors control lighting and water in order to cut down electricity and water consumption by nearly half. The city is touted by the UAE as possibly “one of the world’s most sustainable eco-cities.”

And now University of Birmingham researchers are presenting it as a model to teach the UK and the world about saving energy and resources, contrasting it with energy systems in Birmingham, United Kingdom.

They analyzed the differences and similarities between Masdar, founded very recently in 2008 against an urban environment, and Birmingham, a well-established post-industrial city that has evolved over 400 years. “Masdar City benefits from starting from a blank slate, whereas Birmingham has existing processes, procedures and an ageing infrastructure to negotiate,” according to the researchers.

Masdar is primarily powered by Shams 1, one of the largest concentrated solar power plants in the Middle East, and it houses the Masdar Institute of Science and Technology, which carries out renewable energy research.

“We compared two very different cities – both aspiring to be ‘low-carbon’. Masdar has started well by building low-rise, energy-efficient buildings with smart metering,” says lead author Susan Lee, from the department of civil engineering. “Data from such buildings can help to change people’s behaviour and help develop more energy-efficient new and retrofitted UK buildings. The UAE is a hot and arid place; experience gained in Masdar will help us plan here in the UK for projected hotter summers, with more frequent heatwaves, particularly in cities, as the climate changes.”

Birmingham, says the researcher, has a few things to teach Masdar as well, including how the city adapted to new energy requirements. Lee believes that Masdar can also benefit from her university’s research into hydrogen fuel-cell cars.

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Can garlic-derived creams cure cutaneous leishmanisis?

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A few months after a flesh-eating disease has resurfaced in the Middle East, a research team from Saudi Arabia and Egypt has released a new study which claims that allicin, a sulfur compound found in garlic, can hold the key to a cure.

Leishmaniasis is a protozoal parasitic disease spread by the bite of certain types of sandflies. From cutaneous lesions to fatal visceral infections, the parasite is vicious, but now these scientists are saying that the compound that is derived from the oldest medicinal plant and a cream based on it can heal cutaneous leishmaniasis in mice.

The study published in PLOS One says that at a concentration of 50 micromoles, allicin put on a stopper on the growth of Leishmania parasites. Topical application of allicin cream have successfully reduced lesion sizes.

The scientists studied the toxic effects of allicin on the liver and kidney, but they discovered no significant differences in their biochemical analysis between the control and treated groups.

The potential cure’s promise lies in the fact that it overcomes the disease’s drug resistance, according to the study.

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Detecting deadly foodborne pathogens on the spot

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Researchers from Saudi Arabia and Jordan have invented a cheap sensor that can detect foodborne pathogens within minutes and which can be used by anyone.

The sensor can detect, among other pathogens, Listeria monocytogenes, a notoriously harmful pathogen that has caused numerous infections worldwide and whose inspection and detection efforts exhaust billions of dollars every year, says a new study published in Biosensors & Bioelectronics.

The sensor itself is made of magnetic nanoparticles. It can detect minute traces or serial dilutions of Listeria in milk and meat, as the study demonstrates. “The sensor’s performance is superior in terms of its simplicity, cost and speed,” says researcher Mohammed Zourob, the study’s corresponding author.

Zourob adds that the sensor can be used by non-skilled personnel to check the food contamination; food manufacturers, stores, distributors and even laypersons can use it.

The biosensor changes color from black to yellow in less a minute time when it detects Listeria. Zourob’s team has also developed sensors that can detect other food pathogens such as Escherichia  coli, Salmonella, Shigella flexnerii and Staphylococcus aureus.

Genomes of stone-age woman carry farming tales

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Zagros Mountains harbor a site with evidence for an ancient economy.

Zagros Mountains harbor a site with evidence for an ancient economy.

JTB MEDIA CREATION, Inc. / Alamy Stock Photo

The sequencing of the first genome of an early stone-age woman from Ganj Dareh, in the Iranian Zagros Mountains, can give us a glimpse into the world’s first farming efforts and the evolution of an activity that has profoundly affected human societies.

The international team of scientists, including a researcher from King Abdullah University for Science and Technology (KAUST), Saudi Arabia, has been studying an archaeological site in Zagros – a site with early evidence for an economy of a population of pastoralists, primarily based on goat herding, some 10,000 years ago.

This population has evidently occupied the area for two to three centuries.

Their findings suggest that Western Iran was inhabited by a population genetically similar to hunter-gatherers from the Caucasus, but distinct from the new stone-age Anatolian people who later brought food production into Europe.

The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent.

Archaeobotanical evidence remains limited, according to the study published in Scientific Reports yesterday, but the evidence present gives us an idea into what crops were common: for instance two-row barley with no evidence for wheat or rye.

This probably means that the overall economy was at a much earlier stage in the development of cereal agriculture than that found in the Levant, Anatolia and Northern Mesopotamian basin.