Day: August 24, 2023

Categories : Gender GeneticsTags :

Scientists Finally Create an Accurate Map of the Y Chromosome

On By ModernMedia
Photo by Sangharsh Lohakare on Unsplash

Long overlooked by genetics, the Y chromosome is surprisingly quite challenging to sequence, and so its contributions to health and disease remain largely unknown. For the first time, the complete sequences of 43 human Y chromosomes from lineages from around the globe provides an essential step forward in understanding the roles of the Y chromosome in human evolution and biology. The researchers behind the effort published their findings in two papers in Nature.

Even as the field of human genomics forged ahead at an astonishing pace, the Y chromosome has long remained overlooked. It has been postulated that the human sex chromosomes once originated from a pair of structurally similar chromosomes, but subsequently one of the sex chromosomes, the ancestral Y chromosome, underwent significant degradation, losing 97%of its former complement of genes over many millions of years. This peculiar evolutionary trajectory has given rise to speculation that the human Y chromosomes might eventually disappear completely, albeit millions of years from now, and we already observe that some biological males do lose them in dividing cells as they age, with unclear health consequences.

In practical terms, the Y chromosome contains a large proportion of repetitive and heterochromatic (highly condensed, gene-poor and not transcribed to messenger RNA) sequences, making it exceptionally difficult to fully sequence. Using sequencing methods that can cover long, continuous sequences, the Telomere-to-Telomere (T2T) consortium has now published the first complete Y chromosome assembly from a single individual of European descent in Nature. At the same time, a team led by Jackson Laboratory (JAX) Professor and The Robert Alvine Family Endowed Chair Charles Lee, PhD, FACMG, has published, also in Nature, the assembled Y chromosomes from 43 unrelated males, with nearly half coming from African lineages. These two papers provide intriguing insights into human Y chromosomes, reveal the highly variable nature of Y chromosomes across individuals, and provide an important foundation for future studies on how they may be contributing to certain disorders and diseases.

The need for long reads

Standard short-read genomic sequencing technologies require breaking genomic DNA into short (~250-base-long) fragments. These fragments are then reassembled into the full genome of more than 3 billion base pairs across 46 chromosomes in humans. The method is very accurate and works well for most, but not all, of the genome. Almost all “complete” human genome sequences, including the current reference genome sequence (known as GRCh38), are actually only about 90% complete, because it is difficult to assemble the highly repetitive and other complex sections accurately. GRCh38 falls particularly short for the Y chromosome, as it barely assembles half of that chromosome.

As a result, while the much larger and gene-rich X chromosome has been extensively studied, the Y chromosome has been often overlooked outside of male-based fertility studies. In a significant step forward for the genomics field, scientists from JAX, including first author and JAX Associate Research Scientist, Pille Hallast, PhD, with collaborators from Clemson University, Heinrich Heine University (Germany) and more, have now revealed a full picture of the Y chromosome’s key characteristics and differences between individuals for the first time. Of note is the striking variation in size and structure across the 43 Y chromosomes sequenced that covered 180 000 years of human evolution and range from 45.2 million to 84.9 million base pairs in length.

The inclusion of 43 different individuals representing diverse Y lineages allowed the researchers to redefine inter-chromosomal region boundaries and identify large-scale variations at an unprecedented resolution and clarity. The study also revealed an unexpected degree of structural variation across the Y chromosomes. For example, half of the euchromatin (gene-rich region) of the sequenced chromosomes carries large recurrent inversions (segments that contain the same nucleotide sequences but oriented in the opposite direction) at a rate much higher than anywhere else in the genome. The study further identified regions of the Y chromosome that demonstrate little single nucleotide variation but show high gene copy number variation for specific gene families. Other gene families tended to maintain their copy numbers, however, consistent with their roles in fertility and normal development.

Role in overall health

“Having fully resolved Y chromosome sequences from multiple individuals is essential in order for us to begin to understand how this variation can affect function” says Hallast. “The degree of structural variation between individuals came as a big surprise to me, even though the nucleotide sequences within the Y chromosome genes are comparatively conserved. The variable gene copy numbers in certain gene families and extremely high inversion rates are almost certain to hold significant biological and evolutionary roles.”

The Y chromosome’s contributions to male health are poorly understood. Some unexpected indications of its importance to human health have recently come into focus in two new research studies that collectively implicate the Y chromosome in aggressive features of colorectal and bladder cancers in men. Indeed, one of the studies showed that tumors that had lost the Y chromosomes can more effectively evade T cell immunity, are infiltrated with higher numbers of dysfunctional CD8+ T cells, and are more responsive to anti-PD1 treatments compared to similar tumors retaining the Y chromosome.

“Research is emerging that shows proper Y chromosome gene function is incredibly important for the overall health of men,” says Lee, senior author on the paper. “Our study enables the inclusion of the full Y chromosome in all future studies when sequencing male genomes to understand health and disease.”

Source: Jackson Laboratory

Categories : COVID Medical IndustryTags :

From Molecule to the Shelf

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Bada Pharasi, CEO of The Innovative Pharmaceutical Association of South Africa (IPASA)

Lessons from the COVID-19 pandemic have underlined the importance of continued investment into pharmaceutical innovation and R&D to not only bring life-saving medications to those in need, but to improve public health outcomes, writes Bada Pharasi, CEO of The Innovative Pharmaceutical Association of South Africa (IPASA).

From treatments for cancer, cardiovascular diseases and more recently, the COVID-19 vaccine, the pharmaceutical industry has made significant progress in the development of over 470 medications in the last 10 years alone.1

While the innovative pharmaceutical process typically takes between 10 and 15 years from discovery to regulatory approval2 – owing to factors including immense R&D costs, regulatory compliance, and the protection of patents3 – the fast-tracked development and approval of COVID-19 vaccines laid bare the need for pharmaceutical companies to be prepared to mitigate the risk of future outbreaks – and this means continued investment in innovation and R&D.

The pandemic underlined the need for countries to be prepared for outbreaks on the horizon. To ensure we can meet the next challenge, pharmaceutical innovations must match the pace at which diseases mutate. This kind of innovation is non-negotiable and requires continued investment as a safeguard against losing lives and endangering South Africa’s fragile healthcare system.

As we are in the midst of a cholera epidemic, as well as the recent measles outbreak,4 it’s important to continue driving innovation to treat diseases, with medicines developed by innovative pharmaceutical companies benefiting millions across the country every day.

This is evidenced by mortality rates for HIV/AIDS and TB in the country falling by 59.2% and 55.7% between 2007 and 2017, with at least 60 new medicines currently in the R&D pipeline to treat TB.5

While patents in pharmaceutical innovation protect the originators’ intellectual property, it is important that innovative medications be developed to ensure a continuous pipeline of access to generics once the patent has lost its exclusivity. This will drive consumer accessibility and affordability of life-saving treatments and medications that may otherwise be unattainable for many.

As we continue racing against the proverbial clock in protecting against current and future diseases, pharmaceutical companies should continue to invest in innovation and R&D to outsmart existing dreaded diseases, and provide agility and preparedness should the next unknown pandemic threaten. Our health, and lives, depend on it.

References:
1. #AlwaysInnovating: The pharmaceutical innovation journey [Internet]. IFPMA. 2023 [cited 2023 Jun 28]. Available from: https://www.ifpma.org/initiatives/alwaysinnovating/
2. Derep M. What’s the average time to bring a drug to market in 2022? [Internet]. N-SIDE; 2022 [cited 2023 Jun 28]. Available from: https://lifesciences.n-side.com/blog/what-is-the-average-time-to-bring-a-drug-to-market-in-2022
3. Ancliff S. 10 challenges facing the pharmaceutical industry in 2024 [Internet]. [cited 2023 Jun 29]. Available from: https://blog.i-nexus.com/10-challenges-facing-the-pharmaceutical-industry
4. Yoganathan V. Prepare for more pandemics in the future, experts warn [Internet]. Juta MedicalBrief. Medical Brief; 2023 [cited 2023 Jun 30]. Available from: https://www.medicalbrief.co.za/prepare-for-more-pandemic-in-the-future-experts-warn/
5. South Africa – the innovative hub for pharmaceutical development [Internet]. B2B Central. New Media; 2021 [cited 2023 Jun 29]. Available from: https://www.b2bcentral.co.za/why-south-africa-is-an-innovation-hub-for-pharmaceuticals/

Categories : NeurologyTags :

A Hidden Mathematical Rule Governs the Distribution of Neurons in the Brain

On By ModernMedia
Neuron densities in cortical areas in the mammalian brain follow a consistent distribution pattern. Image: Morales-Gregorio

Human Brain Project (HBP) researchers have uncovered how neuron densities are distributed across and within cortical areas in the mammalian brain. As reported in Cerebral Cortex, they have revealed a fundamental organisational principle of cortical cytoarchitecture: the ubiquitous lognormal distribution of neuron densities.

Numbers of neurons and their spatial arrangement play a crucial role in shaping the brain’s structure and function. Yet, despite the wealth of available cytoarchitectonic data, the statistical distributions of neuron densities remain largely undescribed. This new study from the HBP at Forschungszentrum Jülich and the University of Cologne (Germany) study advances our understanding of the organisation of mammalian brains.

The team accessed 9 publicly available datasets of seven species: mouse, marmoset, macaque, galago, owl monkey, baboon and human. After analysing the cortical areas of each, they found that neuron densities within these areas follow a consistent pattern – a lognormal distribution, pointing to a fundamental organisational principle underlying the densities of neurons in the mammalian brain.

A lognormal distribution is a statistical distribution characterised by a skewed bell-shaped curve. It arises, for instance, when taking the exponential of a normally distributed variable. It differs from a normal distribution in several ways. Most importantly, the curve of a normal distribution is symmetric, while the lognormal one is asymmetric with a heavy tail.

These findings are relevant for modelling the brain accurately. “Not least because the distribution of neuron densities influences the network connectivity,” says Sacha van Albada, leader of the Theoretical Neuroanatomy group at Forschungszentrum Jülich and senior author of the paper. “For instance, if the density of synapses is constant, regions with lower neuron density will receive more synapses per neuron,” she explains. Such aspects are also relevant for the design of brain-inspired technology such as neuromorphic hardware.

“Furthermore, as cortical areas are often distinguished on the basis of cytoarchitecture, knowing the distribution of neuron densities can be relevant for statistically assessing differences between areas and the locations of the borders between areas,” van Albada adds.

These results are in agreement with the observation that surprisingly many characteristics of the brain follow a lognormal distribution. “One reason why it may be very common in nature is because it emerges when taking the product of many independent variables,” says Alexander van Meegen, joint first author of the study. In other words, the lognormal distribution arises naturally as a result of multiplicative processes, similarly to how the normal distribution emerges when many independent variables are summed.

“Using a simple model, we were able to show how the multiplicative proliferation of neurons during development may lead to the observed neuron density distributions” explains van Meegen.

According to the study, in principle, cortex-wide organisational structures might be by-products of development or evolution that serve no computational function; but the fact that the same organisational structures can be observed for several species and across most cortical areas suggests that the lognormal distribution serves some purpose.

“We cannot be sure how the lognormal distribution of neuron densities will influence brain function, but it will likely be associated with high network heterogeneity, which may be computationally beneficial,” says Aitor Morales-Gregorio, first author of the study, citing previous works that suggest that heterogeneity in the brain’s connectivity may promote efficient information transmission. In addition, heterogeneous networks support robust learning and enhance the memory capacity of neural circuits.

Source: Human Brain Project

Categories : Neurodegenerative DiseasesTags :

Study Shows that Intermittent Fasting Might Improve Alzheimer’s Symptoms

On By ModernMedia
Photo by Matteo Vistocco on Unsplash

Circadian disruption is a hallmark of Alzheimer’s disease, affecting nearly 80% of patients with issues such as difficulty sleeping and worsening cognitive function at night. Currently there are no treatments for Alzheimer’s that target this aspect of the disease.

A new study in Cell Metabolism from researchers at University of California San Diego School of Medicine has shown in mice that it is possible to correct the circadian disruptions seen in Alzheimer’s disease with time-restricted feeding, a type of intermittent fasting focused on limiting the daily eating window without limiting the amount of food consumed.

In the study, mice that were fed on a time-restricted schedule showed improvements in memory and reduced accumulation of amyloid proteins in the brain. The authors say the findings will likely result in a human clinical trial.

“For many years, we assumed that the circadian disruptions seen in people with Alzheimer’s are a result of neurodegeneration, but we’re now learning it may be the other way around – circadian disruption may be one of the main drivers of Alzheimer’s pathology,” said senior study author Paula Desplats, PhD, professor at UC San Diego School of Medicine. “This makes circadian disruptions a promising target for new Alzheimer’s treatments, and our findings provide the proof-of-concept for an easy and accessible way to correct these disruptions.”

People with Alzheimer’s experience a variety of disruptions to their circadian rhythms, including changes to their sleep/wake cycle, increased cognitive impairment and confusion in the evenings, and difficulty falling and staying asleep.

“Circadian disruptions in Alzheimer’s are the leading cause of nursing home placement,” said Desplats. “Anything we can do to help patients restore their circadian rhythm will make a huge difference in how we manage Alzheimer’s in the clinic and how caregivers help patients manage the disease at home.”

Boosting the circadian clock is an emerging approach to improving health outcomes, and one way to accomplish this is by controlling the daily cycle of feeding and fasting. The researchers tested this strategy in a mouse model of Alzheimer’s disease, feeding the mice on a time-restricted schedule where they were only allowed to eat within a six-hour window each day. For humans, this would translate to about 14 hours of fasting each day.

Compared to control mice who were provided food at all hours, mice fed on the time-restricted schedule had better memory, were less hyperactive at night, followed a more regular sleep schedule and experienced fewer disruptions during sleep. The test mice also performed better on cognitive assessments than control mice, demonstrating that the time-restricted feeding schedule was able to help mitigate the behavioral symptoms of Alzheimer’s disease.

The researchers also observed improvements in the mice on a molecular level. In mice fed on a restricted schedule, the researchers found that multiple genes associated with Alzheimer’s and neuroinflammation were expressed differently. They also found that the feeding schedule helped reduce the amount of amyloid protein that accumulated in the brain. Amyloid deposits are one of the most well-known features of Alzheimer’s disease.

Because the time-restricted feeding schedule was able to substantially change the course of Alzheimer’s in the mice, the researchers are optimistic that the findings could be easily translatable to the clinic, especially since the new treatment approach relies on a lifestyle change rather than a drug.

“Time-restricted feeding is a strategy that people can easily and immediately integrate into their lives,” said Desplats. “If we can reproduce our results in humans, this approach could be a simple way to dramatically improve the lives of people living with Alzheimer’s and those who care for them.”

Categories : Cardiovascular Disease PaediatricsTags :

Sedentary Time in Children Linked to Later Cardiovascular Damage

On By ModernMedia
Photo by Victoria Akvarel on Pexels

Hours of inactivity during childhood could be setting the stage for heart attacks and strokes later in life, according to research presented at ESC Congress 2023. The large cohort study found that sedentary time accumulated from childhood to young adulthood was associated with heart damage – even in those with normal weight and blood pressure.

“All those hours of screen time in young people add up to a heavier heart, which we know from studies in adults raises the likelihood of heart attack and stroke,” said study author Dr Andrew Agbaje of the University of Eastern Finland, Kuopio, Finland. “Children and teenagers need to move more to protect their long-term health.”

This was the first study to investigate the cumulative effect of smartwatch-assessed sedentary time in young people and cardiac damage later in life. It was conducted as part of the Children of the 90s study, which began in 1990/1991 and is one of the world’s largest cohorts with lifestyle measurements from birth.

At 11 years of age, children wore a smartwatch with an activity tracker for seven days. This was repeated at 15 years of age and again at 24 years of age. The weight of the heart’s left ventricle was assessed by echocardiography, a type of ultrasound scan, at 17 and 24 years of age and reported in grams relative to height (g/m2.7). The researchers analysed the association between sedentary time between 11 and 24 years of age and heart measurements between 17 and 24 years of age after adjusting for factors that could influence the relationship including age, sex, blood pressure, body fat, smoking, physical activity and socioeconomic status.

The study included 766 children, of whom 55% were girls and 45% were boys. At 11 years of age, children were sedentary for an average of 362 minutes a day, rising to 474 minutes a day in adolescence (15 years of age), and 531 minutes a day in young adulthood (24 years of age). This means that sedentary time increased by an average of 169 minutes (2.8 hours) a day between childhood and young adulthood.

Each one-minute increase in sedentary time from 11 to 24 years of age was associated with a 0.004g/m2.7 increase in left ventricular mass between 17 to 24 years of age. When multiplied by 169 minutes of additional inactivity this equates to a 0.7g/m2.7 daily rise, the equivalent of a 3 gram increase in left ventricular mass between echocardiography measurements at the average height gain. A previous study in adults found that a similar increase in left ventricular mass (1g/m2.7) over a seven-year period was associated with a two-fold increased risk of heart disease, stroke, and death.4

Dr. Agbaje said: “Children were sedentary for more than six hours a day and this increased by nearly three hours a day by the time they reached young adulthood. Our study indicates that the accumulation of inactive time is related to heart damage regardless of body weight and blood pressure. Parents should encourage children and teenagers to move more by taking them out for a walk and limiting time spent on social media and video games. As Martin Luther King Jr. once said, ‘If you can’t fly, run. If you can’t run, walk. If you can’t walk, crawl. But by all means keep moving.'”

Source: European Society of Cardiology