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Vijay Chourasia of the LNM Institute of Information Technology in Jaipur and Anil Kumar Tiwari of the Indian Institute of Technology Rajasthan, in Jodhpur, explain how fetal phonocardiography is the modern equivalent of the stethoscope in ante-natal baby care. The team has now adapted this system to be Bluetooth enabled so that fetal heart monitoring can be carried out without repeated intervention and allow data to be analyzed by a personal computer and accessed by healthcare professionals.

The researchers have tested their system on the babies of 33 women at different stages of gestation and compared the data with that obtained by the ultrasound-based Doppler shift technique. The Bluetooth system shows a very high level of accuracy in comparison, 98 percent.

The team points out that using Bluetooth avoids messy cables and the system has a low power consumption, both of which make it portable and easy for mothers-to-be to use without hindrance. Phonocardiography is entirely non-invasive and emits no ultrasound or other energy and so is entirely safe. It should be perfectly amenable to detecting anomalous heart problems at low cost.

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“Wireless data acquisition system for fetal phonocardiographic signals using Bluetooth” in Int. J. Computers in Healthcare, 2012, 1, 240-253

“I knew there would be rare variation but had no idea there would be so much of it,” said the senior author of the research, John Novembre, an assistant professor of ecology and evolutionary biology and of bioinformatics at UCLA.

A team of life scientists studied 202 genes in 14,002 people. The human genome contains some 3 billion base pairs; the scientists studied 864,000 of these pairs. While this is only a small part of the genome, the sample size of 14,002 people is one of the largest ever in a sequencing study in humans.

“Our results suggest there are many, many places in the genome where one individual, or a few individuals, have something different,” Novembre said. “Overall, it is surprisingly common that there is a rare variant in the population.

“This study doesn’t tell us how to cure a particular disease but suggests that disease in general may be caused by rare variants, and if you’re trying to find the genetic basis of disease, it’s important to focus on those variants. Understanding the genetic basis of disease provides clues to how the diseases work and clues about how to treat them.”

The scientists discovered one genetic variant every 17 bases, which was a dramatically higher rate than they expected, said Novembre, a population geneticist who is a member of UCLA’s interdepartmental program in bioinformatics.

Most of the time, only one person has the genetic variant and the other 14,001 do not.

“We saw lots of that,” he said. “We discovered there are many places in these 202 genes where there is variation and only a few individuals differ from the whole group, or only one differs. We also see evidence that a substantial fraction of these rare genetic variants appear to be deleterious in a long-term evolutionary sense and might impact disease.”

The research team included Daniel Wegmann, a former UCLA postdoctoral scholar in Novembre’s laboratory and a co-first author of the study; Darren Kessner, a UCLA graduate student in the bioinformatics interdepartmental Ph.D. program; colleagues from the University of Michigan, Ann Arbor (in fields including human genetics and biostatistics); and geneticists from international health care company GlaxoSmithKline, including project leader Matthew Nelson. The UCLA life scientists were involved in the population genetic analysis of the data.

In the study, 10,621 people had one of 12 diseases, including coronary artery disease, multiple sclerosis, bipolar disorder, schizophrenia, osteoarthritis and Alzheimer’s disease; 3,381 did not have any of the diseases.

“The large sample size allows us to see patterns with more clarity than ever before,” Novembre said. “If rare variants are like distant stars, this kind of large sample size is like having the Hubble Telescope; it’s allowing us to see more than before. We see a ton of rare variation, and these rare variants more often make changes to proteins than not. In that way, this study has important implications for the genetic basis of disease in humans. It’s consistent with the idea that many diseases may be partly caused by rare variants.”

Human population growth helps to explain the large number of genetic variants, the scientists said.

“The fact that we see so many rare variants is in part due to the fact that human populations have been growing very rapidly,” Novembre said. “Because the human population has grown so much, the opportunity for mutations to occur has also grown. Some of the variants we are seeing are very young, dating to population growth since the invention of agriculture and even the Industrial Revolution; this growth has created many opportunities for mutation in the genome because there are so many transmissions of chromosomes from parent to child in large populations.”

The scientists isolated and sequenced the pieces of DNA from the 202 genes.

They estimated mutation rates from population genetic data, which has only rarely been done before.

“We have been able to estimate mutation rates for each of the genes, which has been difficult to do with smaller sample sizes,” Novembre said. “In future research, we can study mutation rates not just in these 202 genes, but genome-wide.”

Sequencing technologies are advancing rapidly, he said. “What seemed like science fiction in the past is science today.”

Rare genetic variants would not have been detectable in most previous studies, whose samples usually had fewer than 1,000 people.

Typically, in population genetics, it is difficult to estimate mutation rates separately from population sizes, but when you get to very large sample sizes, you can estimate the two separately, Novembre said.

“We estimate 202 mutation rates, one for each gene,” he said. “We show that the mutation rate varies from gene to gene. Follow-up studies may be able to reveal more about what factors affect mutation rates.”

Rare genetic variants are frequently geographically localized to small pockets around the globe rather than being widespread, Novembre said.

In the image accompanying this release, each vertical line represents one of the 202 genes. For each gene, the scientists plotted, at the top of the image, the number of genetic variants that have a frequency greater than 0.5 percent. When variants are greater than 0.5 percent, previous studies have been able to find most of them.

“With our large sample size, we can detect variants at a frequency less than 0.5 percent, and we see all of these, which have never been seen before,” Novembre said. “Previous studies have examined the tip of the iceberg of genetic variation, but there is all this rare variation that has been below the surface, below our threshold of detection. Now, with large sample sizes, we can see a more complete picture of human genetic diversity.”

The genetic code has changes that are “nonsynonymous” (they change the meaning of a protein) and “synonymous” (they don’t change the meaning of a protein).

“We see many nonsynonymous changes amongst the rare variants, and these are plausibly affecting disease in humans, though in ways that are not yet well understood,” Novembre said.

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Methods: In the present study, we analyzed the 3′-untranslated region (UTR) of Leishmania HSP70-type I gene from 24 strains representing eleven Leishmania species in the belief that this non-coding region would have a better discriminatory capacity for species typing than coding regions. Results: It was observed that there was a remarkable degree of sequence conservation in this region, even between species of the subgenus Leishmania and Viannia. In addition, the presence of many microsatellites was a common feature of the 3′-UTR of HSP70-I genes in the Leishmania genus.

Finally, we constructed dendrograms based on global sequence alignments of the analyzed Leishmania species and strains, the results indicated that this particular region of HSP70 genes might be useful for species (or species complex) typing, improving for particular species the discrimination capacity of phylogenetic trees based on HSP70 coding sequences. Given the large size variation of the analyzed region between the Leishmania and Viannia subgenera, direct visualization of the PCR amplification product would allow discrimination between subgenera, and a HaeIII-PCR-RFLP analysis might be used for differentiating some species within each subgenera.

Conclusions: Sequence and phylogenetic analyses indicated that this region, which is readily amplified using a single pair of primers from both Old and New World Leishmania species, might be useful as a molecular marker for species discrimination.
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Findings:

We compared host-seeking behavior in one group of emerging female adults treated with L-beta-3,4-dihydroxyphenylalanine (L-DOPA), the precursor of DA, (L-DOPA group), with that in an untreated control (control group) after confirming elevation of head DA in L-DOPA group by using high-performance liquid chromatography. The content of head DA in L-DOPA group significantly remained higher than that in controls on all days examined. The host-seeking activity in the control group showed a gradual increase over the 6-day experimental period. In contrast, there was no such increase in the host-seeking activity in the L-DOPA group. Therefore, the host-seeking activity of L-DOPA group was significantly lower than that of the controls between day 3 and 6 post-emergence.

Conclusion:
Our results indicate that elevation of DA level reduces host-seeking activity in adult female mosquito Ae. albopictus.
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Gordon’s research first established a link between obesity and the trillions of friendly microbes that live in the intestine, where they extract nutrients and calories from food. His studies have shown that diet helps shape the mix of microbes in the intestine and that these microbes, in turn, influence how efficiently nutrients and calories are harvested from foods. This dynamic interplay has led Gordon to suspect that an imbalance of certain types of gut microbes conspires with an inadequate diet to trigger malnutrition.

“A complex relationship exists between diet, gut microbial communities and the immune system in severely malnourished children,” says Gordon, the Dr. Robert J. Glaser Distinguished University Professor and director of Washington University’s Center for Genome Sciences and Systems Biology. “We now have a way to tease apart these influences. This project seeks to discover novel dietary and microbial therapeutics that can be targeted to infants and children living in countries with rampant malnutrition.”

Severe malnutrition has long been thought to stem simply from a lack of adequate food. But now scientists understand the condition is far more complex and may involve a breakdown in the way gut microbes process various components of the diet.

The community of intestinal microbes and their vast collection of genes, known as the gut microbiome, are assembled right from birth and influenced by babies’ early environments and the first foods they consume, such as breast milk. As part of the Breast Milk, Gut Microbiome and Immunity Project, Gordon will work with other scientists to evaluate the relationship among first foods, the developing community of microbes in the intestine and the developing immune system.

The new research builds on ongoing clinical studies in Africa, South Asia and South America of malnourished and healthy infants and children and their mothers. Gordon has played a key role in that research, which also is funded by the Gates Foundation.

As part of the new project, scientists will evaluate the function of gut microbial communities in malnourished and healthy infants and children living in countries where malnutrition is prevalent. They also will characterize the nutritional content and immune activity present in breast milk samples obtained from the children’s mothers during periods of exclusive and supplemental breastfeeding. In parallel, the scientists will use a preclinical discovery pipeline recently developed in Gordon’s laboratory to identify next-generation probiotics and nutrient supplements or combinations of the two (synbiotics) that may promote healthy growth in infants and children.

The investigators also will transplant communities of intestinal microbes, obtained from stool samples, from both malnourished and healthy children into germ-free mice raised under sterile conditions. These mice will harbor collections of human gut microbes that mimic those found in the children, and they will be fed the same diets as the children.

Then, using the mice, Gordon and his colleagues can carefully evaluate how various nutritional interventions influence gut microbiomes obtained from these children. They will be able to determine which microbes respond, how they respond and how they affect the overall function of the gut microbial communities. The researchers also will evaluate certain aspects of childhood development.

“It’s extremely difficult to study individual triggers for malnutrition because there are so many variables to consider,” Gordon says. “Recreating the human gut ecosystem in mice gives us a way to control these variables. The lead compounds derived from these well-controlled, pre-clinical studies then can be considered for future clinical trials in malnourished infants and children.”

Gordon’s research underscores the need understand the workings of gut microbiomes among people of different ages living in different parts of the world, especially as scientists consider manipulating intestinal microbes to improve health and nutrition. In a study published online May 9 in Nature, he and his colleagues surveyed the gut microbiomes of more than 500 healthy individuals, ranging in age from one month to more than 80 years, who lived in villages in Malawi, the Amazon region of Venezuela and in three U.S. cities.

The researchers found a similarity across cultures in the way the gut microbiome matures, especially in the first three years of life. But they also noted distinct differences in the microbiomes of babies, children and adults depending on where they lived.

The differences were most notable between individuals living in the U.S. compared to those in Malawi or Venezuela, and seemed to be linked to diet. Malawian and Venezuelan gut communities were rich in genes that break down complex sugars and starches, like those found in cassava and corn, while gut communities in individuals in the U.S., who typically eat high-protein diets, were more heavily loaded with genes for breaking down amino acids.

Other scientists involved in the Gates Foundation project include: Per Ashorn, MD, PhD, at the University of Tampere School of Medicine in Finland; Kathryn Dewey, PhD, University of California, Davis; Michael Gottlieb, PhD, Foundation for the National Institutes of Health (NIH); Rob Knight, PhD, University of Colorado, Boulder; Kenneth Maleta, PhD, University of Malawi College of Medicine; David Mills, University of California, Davis; Jeremy Nicholson, PhD, Imperial College, London; Linda Saif, PhD, The Ohio State University.

Results:
The behaviour of M and S form larvae was found to differ significantly; although both forms mainly foraged at the water surface, spending 60-90% of their time filtering water at the surface or along the wall of the container, M form larvae spent on average significantly more time browsing at the bottom of the container than S form larvae (4.5 vs. 1.3% of their overall time, respectively; P < 0.05). In the presence of a predator, larvae of both forms modified their behaviour, spending significantly more time resting along the container wall (P < 0.001). This change in behaviour was at least twice as great in the M form (from 38.6 to 66.6% of the time at the wall in the absence and presence of the predator, respectively) than in the S form (from 48.3 to 64.1%). Thrashing at the water surface exposed larvae to a significantly greater risk of predation by the notonectid (P < 0.01), whereas predation occurred significantly less often when larvae were at the container wall (P < 0.05) and might reflect predator vigilance.
Conclusions:
Behavioural differences between larvae of the M and S form of An. gambiae in response to an acute predation risk is likely to be a reflection of different trade-offs between foraging and predator vigilance that might be of adaptive value in contrasting aquatic ecosystems. Future studies should explore the relevance of these findings under the wide range of natural settings where both forms co-exist in Africa.
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