Daily Archives: 29 May 2024

The unveiling of a newly sequenced genome offers profound insights into the ancient origins of coffee and its prospective trajectory in the face of climate change

Unlocking the potential for cultivating coffee plants resilient to climate change in the forthcoming decades may trace its roots back to ancient times.

A collaborative effort spearheaded by the University at Buffalo has yielded what is proclaimed the most superior reference genome for Arabica, the world’s most favoured coffee species. This feat has unearthed a wealth of knowledge regarding its lineage, spanning millennia and continents, shedding light on its evolutionary journey. The findings, published in Nature Genetics, unveil that Coffea arabica emerged over 600,000 years ago in the Ethiopian forests through natural hybridisation between two other coffee species. The population of Arabica underwent fluctuations across Earth’s climatic oscillations over thousands of years before being cultivated in Ethiopia and Yemen and subsequently disseminated globally.

“We’ve utilised genomic data from contemporary plants to delve into the past and construct the most precise narrative possible of Arabica’s extensive history, while also elucidating the relationships among modern cultivated varieties,” remarks Victor Albert, PhD, co-corresponding author of the study and Empire Innovation Professor in the UB Department of Biological Sciences.

Major coffee corporations such as Starbucks and Tim Hortons rely exclusively on Arabica beans for their millions of daily servings. However, Arabica’s susceptibility to pests and diseases stems from its low genetic diversity due to a history of inbreeding and small population size, which limits its cultivation to regions with lower pathogen threats and favourable climatic conditions.

“An intricate understanding of the origins and breeding history of contemporary varieties is imperative for developing new Arabica cultivars better suited to withstand climate change,” adds Albert.

Employing cutting-edge DNA sequencing technology and advanced data science, the research team accomplished the sequencing of 39 Arabica varieties and even an 18th-century specimen used by Swedish naturalist Carl Linnaeus to classify the species. The reference genome is now accessible in a publicly available digital database.

“While other public references for Arabica coffee do exist, the quality of our team’s work is exceptionally high,” notes Patrick Descombes, senior expert in genomics at Nestlé Research and one of the study’s co-leaders.

Humanity’s adoration for coffee evolved without human intervention. Arabica originated as a natural hybridisation between Coffea canephora and Coffea eugenioides, receiving genetic contributions from both parents. This event’s precise timing and location have long been debated, with estimates ranging from 10,000 to 1 million years ago.

To pinpoint evidence of this pivotal event, UB researchers and collaborators employed computational modelling to scrutinise various Arabica genomes for signatures of its foundation. The models delineate three population bottlenecks in Arabica’s history, with the oldest occurring approximately 610,000 years ago, suggesting that Arabica formed sometime before that, potentially between 610,000 to 1 million years ago.

“In essence, the formation of Arabica was a natural occurrence predating modern humans and the domestication of coffee,” asserts Albert.

Coffee plants have traditionally been believed to have originated in Ethiopia. However, the study’s examination of wild varieties collected around the Great Rift Valley reveals a distinct geographical split: wild varieties originated from the western side. In contrast, cultivated varieties originated from the eastern side near the Bab al-Mandab strait separating Africa and Yemen. This aligns with evidence suggesting that coffee cultivation likely commenced primarily in Yemen around the 15th century.

“It appears that Yemeni coffee diversity may serve as the progenitor of all major current varieties,” observes Descombes.

The study juxtaposes climate events with fluctuations in wild and cultivated Arabica populations over time. Modelling indicates a prolonged period of low population size between 20,000 and 100,000 years ago, corresponding to an extended drought and cooler climate in the region. The population surged approximately 6,000 to 15,000 years ago during the African humid period, coinciding with more favourable growth conditions. Around 30,000 years ago, wild varieties and those destined for human cultivation diverged.

Cultivated Arabica faces a looming threat due to its low genetic diversity. It is estimated to have an adequate population size of only 10,000 to 50,000 individuals. This vulnerability leaves it susceptible to decimation by pathogens such as coffee leaf rust, which causes annual losses of $1-2 billion.

The reference genome unveils insights into how one line of Arabica varieties acquired robust resistance to disease. The Timor variety, originating in Southeast Asia as a spontaneous hybrid between Arabica and its parent, Coffea canephora, possesses more excellent disease resistance than Arabica.

“Consequently, when Robusta hybridised back into Arabica on Timor, it brought along some of its pathogen defence genes,” explains Albert.

While breeders have endeavoured to replicate this crossbreeding to enhance pathogen resistance, the new Arabica reference genome has enabled researchers to pinpoint a novel region housing members of the RPP8 resistance gene family and a general regulator of resistance genes, CPR1.

“These findings indicate a novel target locus for potentially enhancing pathogen resistance in Arabica,” remarks Jarkko Salojärvi, assistant professor at Nanyang Technological University and co-corresponding author of the study.

Furthermore, the genome reveals other novel discoveries, including the closest wild varieties to modern cultivated Arabica and the likely parentage of the Typica variety. This early Dutch cultivar is believed to be the progenitor of the Bourbon variety.

“Our endeavour has been akin to reconstructing the genealogical tree of a highly significant family,” concludes Albert.

More information: Jarkko Salojärvi et al, The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars, Nature Genetics. DOI: 10.1101/2023.09.06.556570

Journal information: Nature Genetics Provided by University at Buffalo

Researchers have pinpointed specific targets within the brain that can be modulated to regulate heart rate and potentially alleviate depressive disorders

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A recent investigation led by researchers at Brigham and Women’s Hospital, a prominent member of the Mass General Brigham healthcare system, indicates that heart rate could serve as a valuable indicator for determining optimal brain stimulation sites in individuals with depressive disorders when conventional brain imaging techniques are unavailable.

The study, featured in Nature Mental Health, examined data from 14 individuals exhibiting no symptoms of depression. By utilising transcranial magnetic stimulation (TMS) to target specific brain regions associated with depression, researchers observed concurrent effects on heart rate. This suggests that clinicians may identify and target relevant brain areas without the necessity of widely inaccessible brain scans.

Senior author Dr Shan Siddiqi of Brigham’s Department of Psychiatry and the Center for Brain Circuit Therapeutics explained that the concept emerged during a conference where Dutch researchers presented data on heart-brain coupling. The findings indicated the transient reduction of heart rate through TMS and the significance of the stimulation site. Dr. Siddiqi expressed enthusiasm for providing easier access to precision-targeted depression treatment worldwide, leveraging advanced technology in Boston.

Collaborating with colleagues at the Center for Brain Circuit Therapeutics, lead author Eva Dijkstra, MSc, integrated their expertise on heart-brain coupling with Brigham’s research on brain circuitry. This collaborative effort led to the identification of ten brain spots in each participant, categorised as either optimal (‘connected areas’) or non-optimal for depression treatment, with subsequent observation of heart rate fluctuations upon stimulation of each spot.

Dijkstra highlighted the promising discovery, emphasising the substantial heart-brain coupling observed in the connected areas for most participants. This finding holds the potential for customising TMS therapy based on individual brain targets, a development that could significantly improve the lives of individuals with depressive disorders, without the prerequisite of an MRI scan.

Dr. Siddiqi underscored the study’s broader implications, foreseeing its relevance in developing treatments applicable to cardiologists and emergency physicians in clinical settings. However, the study’s limitations lie in its small sample size and the inability to stimulate all possible brain spots.

Moving forward, the team is optimistic about refining their understanding of brain stimulation sites to ensure consistent changes in heart rate. Meanwhile, Dijkstra’s team in the Netherlands is conducting a larger study involving 150 individuals with treatment-resistant depression, with data analysis expected to significantly advance the research’s clinical translation later this year.

More information: Eva S. A. Dijkstra et al, Probing prefrontal-sgACC connectivity using TMS-induced heart–brain coupling, Nature Mental Health. DOI: 10.1038/s44220-024-00248-8

Journal information: Nature Mental Health Provided by Brigham and Women’s Hospital

The foodborne pathogen Listeria can evade sanitizers by concealing itself within biofilms

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The Centers for Disease Control and Prevention highlight that every year in the U.S., approximately 1,600 individuals contract a severe infection from Listeria bacteria present in food, with around 260 fatalities reported annually. Researchers from Penn State have deepened our understanding of how these bacteria, specifically Listeria monocytogenes, persist and thrive in fruit-packing environments by resisting sanitisation efforts.

Their findings, soon to be published in the June edition of the journal Biofilm and currently accessible online, reveal how biofilms—structures formed by benign microorganisms that cluster together and adhere to surfaces—create a protective barrier around the Listeria. According to the research team, this barrier shields the bacteria from sanitisers, potentially leading to significant revisions in cleaning procedures at food-processing facilities aimed at reducing Listeria contamination.

Jasna Kovac, the Lester Earl and Veronica Casida Career Development Professor of Food Safety and the study’s corresponding author, explained that they identified two specific groups of microorganisms, Pseudomonadaceae and Xanthomonadaceae, which are particularly adept at forming these biofilms. These biofilms not only physically obstruct the sanitisers, making them less effective, but are also believed to enhance Listeria’s resistance to the antimicrobial agents commonly used in these facilities.

Laura Rolon, a recent Penn State doctoral graduate and the lead researcher, noted that these biofilms significantly undermine sanitisers’ efficacy against Listeria monocytogenes. The study suggests that facilities experiencing recurrent issues with this pathogen should evaluate whether these biofilm-forming microorganisms are a contributing factor.

Kovac further stated that their findings necessitate a review of the effectiveness of sanitisers against these non-pathogenic, biofilm-forming microorganisms typically found in food processing environments. This could lead to better strategies to prevent biofilm formation, thus enhancing control over Listeria monocytogenes. Future assessments might yield practical recommendations for the industry, such as optimal concentrations and sanitiser application durations.

Luke LaBorde, a professor of food science, extension specialist, and co-author of the study, emphasised the importance of disseminating these findings to those involved in sanitation at food-processing facilities. He pointed out that Penn State Extension is committed to translating scientific research into practical applications through workshops and short courses aimed at professionals in the tree-fruit industry. These efforts are designed to improve sanitation practices and effectively manage the risk of Listeria monocytogenes.

These educational initiatives by Penn State Extension serve as a bridge between scientific discoveries and their application in the field, reflecting the core mission of a land-grant university like Penn State. The university aims to communicate crucial research findings through regular workshops and other resources, such as those on Listeria monocytogenes and biofilms, and promote best practices for controlling foodborne pathogens. These sessions are typically attended by professionals from food-processing plants, industry association representatives, food safety consultants, and government inspectors, all geared towards enhancing food safety across the industry.

More information: M. Laura Rolon et al, Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride, Biofilm. DOI: 10.1016/j.bioflm.2024.100177

Journal information: Biofilm Provided by Penn State

A Rutgers Health Study Reveals the Vital Role of Social Networks in Supporting Older Adults Living with HIV

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In a study featured in AIDS Care and spearheaded by Kristen Krause, an instructor at the Rutgers School of Public Health, an examination was conducted into the social networks of older individuals grappling with HIV in Newark, N.J. – a locale often sidelined in research focused on this demographic. “This study is instrumental in deciphering the impact of support networks on older adults contending with HIV and how the presence of stigma and fractured relationships can pave the way for adverse health outcomes,” remarked Krause. She highlighted that many studies concentrate on more significant urban hubs like New York, Los Angeles, and San Francisco.

With a staggering 1.2 million individuals living with HIV in the United States, advancements in medical technology have stretched their lifespans, challenging the notion of HIV primarily afflicting young demographics. The Centers for Disease Control and Prevention underscore that half of those living with the virus in the United States are aged 50 or above, underlining the significance of grasping the dynamics of social support for this cohort. Older individuals grappling with HIV often confront stigma tied to both their HIV status and advancing age, which can impinge upon their mental well-being and escalate social seclusion.

Assistance from diverse sources such as community organisations, family, and healthcare providers proves pivotal in mitigating these hurdles, furnishing avenues for connection and encouragement towards self-care. Research indicates that social support not only acts as a buffer against stigma but also diminishes levels of stress, anxiety, and depression among older individuals living with HIV. “Social support stands as a pivotal element in resilience and surmounting formidable obstacles that older adults dealing with HIV may encounter,” affirmed Krause.

“Social support stands as a pivotal element in resilience and surmounting formidable obstacles that older adults dealing with HIV may encounter,” affirmed Krause. “It can manifest in various forms, ranging from friendships and familial bonds to support groups, each serving distinct yet collective roles in ensuring favourable health outcomes in older individuals grappling with HIV.” Researchers enlisted 40 participants aged 51 to 69 through diverse sampling methods within the Newark metropolitan area, encompassing drag shows, pride events, and medical facilities.

From the amassed data, four principal themes surfaced regarding participants’ experiences navigating life with HIV as older individuals: friendships and relationships, support groups, stigma and discrimination, and family, all of which underscored the recurring significance of social support. The study’s findings underscore the imperative for older adults contending with HIV to foster robust support systems, particularly in underexplored regions such as Newark. The absence of such networks correlated with a spectrum of challenges among participants as they age, including heightened substance use, depressive episodes, anxiety, homelessness, and adverse health outcomes.

“It is imperative for researchers and public health practitioners to collaborate in devising programmes that can facilitate consistent and affirming interactions for older adults grappling with HIV,” emphasised Krause. “This will significantly enhance the overall quality of life for many individuals and bolster positive health outcomes.” Looking forward, Krause emphasised the necessity for further research tailored to this demographic, advocating for augmented funding and the formulation of interventions and programmes that nurture social support through dependable and affirmative experiences, given that not all older adults living with HIV have seamless access to such support and resources.

More information: Susannah C. Gervolino et al, The role of social support networks in a sample of older adults living with HIV: the GOLD studies, AIDS Care. DOI: 10.1080/09540121.2024.2312877

Journal information: AIDS Care Provided by Rutgers University