It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Tuesday, April 09, 2024
Understanding the link between family physician characteristics and COVID-19 vaccination gaps
CANADIAN MEDICAL ASSOCIATION JOURNAL
New research examining the characteristics of physicians with the largest share of patients unvaccinated against SARS-CoV-2 may help increase vaccination rates going forward. The study, published in CMAJ (Canadian Medical Association Journal) https://www.cmaj.ca/lookup/doi/10.1503/cmaj.230816, found that family physicians in Ontario with the largest percentage of unvaccinated patients generally served patients living in marginalized neighbourhoods and had less support in their practices.
Researchers analyzed linked data on 9060 family physicians with more than 10 million enrolled patients and calculated the percentage of patients unvaccinated against SARS-CoV-2 per physician. They compared family physicians (n = 906) caring for the largest proportion of unvaccinated patients (top 10%) with the rest of the comprehensive-care family physicians in Ontario. They found the group with the largest proportion of unvaccinated patients were more likely to be male, to have trained outside Canada, to be older (mean age of 56 v. 49 years), and to work in a fee-for-service model than the remaining 90% of physicians.
“The family physicians with the most unvaccinated patients were also more likely to be solo practitioners and less likely to practise in team-based models, meaning they may have fewer support staff in their clinics,” says Dr. Jennifer Shuldiner, lead author and scientist, Women’s College Hospital, Toronto, Ontario. “This illustrates the ongoing inverse relationship between the need for care, and its accessibility and utilization. In other words, the practices with the highest need receive the fewest resources.”
As many of the physicians with the largest percentage of unvaccinated patients served people living in marginalized neighbourhoods, awareness of cultural differences in perspectives on vaccination should be considered.
“Many marginalized communities have a history of neglect from government (municipal, provincial, federal) and health care, and this may lead to mistrust in public health initiatives,” the study authors write. “Interventions to support these communities should include meaningful community engagement and consideration for age-, language-, and culturally appropriate communication tools to assist primary care in boosting vaccine uptake.”
Although the majority of SARS-CoV-2 vaccines were not administered by family physicians, clinicians have an important role to play in educating patients about the benefits of vaccination.
“We know that relationships with trusted family physicians can positively influence patients’ decisions,” explains Dr. Noah Ivers, senior author and clinician scientist, Women’s College Hospital. “Our study highlights the need to create equitable systems and processes that create opportunities for primary care teams to play a crucial role in influencing both general and SARS-CoV-2-specific vaccine-related decision-making.”
Expanding primary care teams in marginalized neighbourhoods and using hotspot strategies to focus public health resources in under-vaccinated communities could help support public health initiatives like vaccination.
Characteristics of primary care practices by proportion of patients unvaccinated against SARS-CoV-2: a cross-sectional cohort study
Bringing multidrug-resistant pathogens to their knees
Fluorous lipopetides act as highly effective antibiotics
WILEY
Multidrug-resistant bacterial infections that cannot be treated by any known antibiotics pose a serious global threat. In the journal Angewandte Chemie, a Chinese research team has now introduced a method for the development of novel antibiotics to fight resistant pathogens. The drugs are based on protein building blocks with fluorous lipid chains.
Antibiotics are often prescribed far too readily. In many countries they are distributed without prescriptions and administered in factory farming: prophylactically to prevent infections and enhance performance. As a result, resistance is on the rise—increasingly against reserve antibiotics as well. The development of innovative alternatives is essential.
It is possible to learn some lessons from the microbes themselves. Lipoproteins, small protein molecules with fatty acid chains, are widely used by bacteria in their battles against microbial competitors. A number of lipoproteins have already been approved for use as drugs. The common factors among the active lipoproteins include a positive charge and an amphiphilic structure, meaning they have segments that repel fat and others that repel water. This allows them to bind to bacterial membranes and pierce through them to the interior.
A team led by Yiyun Cheng at East China Normal University in Shanghai aims to amplify this effect by replacing hydrogen atoms in the lipid chain with fluorine atoms. These make the lipid chain simultaneously water-repellant (hydrophobic) and fat-repellant (lipophobic). Their particularly low surface energy strengthens their binding to cell membranes while their lipophobicity disrupts the cohesion of the membrane.
The team synthesized a spectrum (substance library) of fluorous lipopeptides from fluorinated hydrocarbons and peptide chains. To link the two pieces, they used the amino acid cysteine, which binds them together via a disulfide bridge. The researchers screened the molecules by testing their activity against methicillin-resistant Staphylococcus aureus (MRSA), a widespread, highly dangerous strain of bacteria that is resistant to nearly all antibiotics. The most effective compound they found was “R6F”, a fluorous lipopeptide made of six arginine units and a lipid chain made of eight carbon and thirteen fluorine atoms. To increase biocompatibility, the R6F was enclosed within phospholipid nanoparticles.
In mouse models, R6F nanoparticles were shown to be very effective against sepsis and chronic wound infections by MRSA. No toxic side effects were observed. The nanoparticles seem to attack the bacteria in several ways: they inhibit the synthesis of important cell-wall components, promoting collapse of the walls; they also pierce the cell membrane and destabilize it; disrupt the respiratory chain and metabolism; and increase oxidative stress while simultaneously disrupting the antioxidant defense system of the bacteria. In combination, these effects kill the bacteria—other bacteria as well as MRSA. No resistance appears to develop.
These insights provide starting points for the development of highly efficient fluorous peptide drugs to treat multi-drug resistant bacteria.
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About the Author
Dr. Yiyun Cheng is Professor of Materials Chemistry and Biotechnology at the School of Life Sciences, East China Normal University. His research interests focus on the rational design of biomaterials for cytosolic delivery of biomacromolecules such as DNA, RNA, protein and peptide.
Coral farming based on sexual propagation, leading to a more sustainable coral trade and helping to protect coral reefs – this is the goal of SciReef, a new start-up which is emerging from a research transfer project. SciReef is based on the research conducted by Dr Samuel Nietzer and Dr Mareen Möller in the Environmental Biochemistry research group at the Wilhelmshaven site of the University of Oldenburg’s (Germany) Institute for Chemistry and Biology of the Marine Environment (ICBM). The Federal Ministry for Economic Affairs and Climate Action (BMWK) and the European Social Fund Plus (ESF Plus) support the innovative start-up with around 920,000 euros in EXIST Transfer of Research funding over the next two years. Peter Schupp, Professor of Environmental Biochemistry at the ICBM, will be the start-up’s scientific mentor. The project will receive additional support from the university's Founding and Innovation Center (GIZ). The researchers are also collaborating with Tropic Marin AG, a seawater aquarium supplies company based in Hünenberg (Switzerland).
SciReef wants to propagate stony corals via natural reproduction
“We are delighted about the funding and hope to be able to build a sustainable company that will contribute to the protection of wild corals,” said Nietzer, the future managing director of SciReef. In addition to covering the personnel costs for three scientific and one administrative member of staff, the funding includes around 250,000 euros to cover material costs such as chemicals, equipment and consumables. With its EXIST programme, the BMWK supports innovative, sustainable spin-offs that involve high-risk resource development at universities and other research institutions.
SciReef’s goal is to propagate stony corals via their natural sexual reproduction process and then grow out the young corals in aquaria. Commercial production of corals using sexual propagation methods has not been possible to date, meaning that the trade in corals currently relies on the asexual fragmentation technique and wild harvesting, which can pose a problem for reefs at the local level. If the project succeeds, it could lead to the global coral trade becoming considerably more environmentally sustainable and less reliant on wild harvesting. To protect their reefs, many countries have imposed export restrictions which, together with the rising logistics costs, are making the coral trade increasingly expensive. An additional advantage of the sexual reproduction technique is that it allows the breeding of corals with specific characteristics, for example new colour variants that don’t occur in nature. Compared to fragmentation, the most commonly used method to produce corals, in which a large coral is split into a number of smaller ones, sexual reproduction leads to a much higher genetic diversity. Fragmented corals, on the other hand, are clones and thus identical to the original colony.
Oldenburg scientists were first in Germany to successfully breed stony corals via sexual reproduction
The researchers will build on the basic techniques developed in the course of their earlier research. A few years ago, they became the first team of scientists in Germany to successfully breed stony corals in the lab through sexual reproduction. The young corals thus produced are much better adapted to aquarium conditions than those imported from tropical oceans.
One critical aspect of the new production method envisaged by SciReef will be to improve the “settlement” process in which the free-swimming coral larvae attach to a solid substrate. The experts plan to use chemical compounds that prompt the larvae to settle on specially designed artificial substrates. Over the last 15 years the Environmental Biochemistry research group has been able to isolate and identify one such compound.
Another equally decisive factor will be finding ways to improve the conditions for the young corals’ development once they have settled, since they are particularly fragile at this early stage. To this end, SciReef plans to optimise key factors such as nutrition, lighting and the chemical composition of the water in the aquariums and inoculate the young corals with special microalgae in order to improve survival rates.
A female stony coral releases eggs into the water. Together with the sperm that the male coral also releases into the water, this process is the basis for the sexual reproduction of corals.
CREDIT
University of Oldenburg / Samuel Nietzer
A spawning stony coral Acropora. Thousands of small eggs float above the coral in the water.
CREDIT
University of Oldenburg / Mareen Möller
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Animals
Unlocking the genetic secrets of Pterocarya hupehensis: a phylogeographic study on the impact of environmental changes and geographical barriers
MAXIMUM ACADEMIC PRESS
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DISTRIBUTION OF 24 CHLOROPLAST HAPLOTYPES OF PTEROCARYA HUPEHENSIS.
Environmental factors and geographical barriers have historically shaped species' genetic structures, with the Sino-Japanese Floristic Region and Sichuan Basin being key study areas. Research has highlighted the role of the Qinghai-Tibet Plateau uplift and East Asian monsoon on biodiversity, yet the dynamics of species around the Sichuan Basin during the Miocene climate change, and how species characteristics and geographic barriers affected their genetic patterns remains underexplored. Most phylogeographic studies focus on chloroplast DNA, overlooking pollen-mediated gene flow in wind-pollinated species like the conservation-concerned Pterocarya hupehensis. This gap underscores the need for studies incorporating species-specific traits and gene flow mechanisms to enhance our understanding of phylogeographic patterns.
To investigate the phylogeographic history of Pterocarya hupehensis, researchers employed cpDNA sequence variation analysis, RAD-seq reads for nuclear DNA analysis, and ecological niche modeling. The cpDNA analysis revealed 91 polymorphisms and 24 haplotypes across 17 populations. The phylogenetic network resolved two main haplotype lineages (western and eastern lineages) and a divergence dating back to the middle Miocene (16.7 Mya). RAD-seq analysis of 122 samples identified 2,889 SNPs. Admixture analysis revealed that the genetic structure of P. hupehensis consisted of two lineages and detected genetic introgression in five populations. The researchers further analyzed the population demographic histories by ML tree, and found two strong signals with a high migration weight, indicating unidirectional gene flow in populations. Ecological niche modeling suggested that P. hupehensis population expansion occurred during the last interglacial period and suitable area for P. hupehensis in the western and southern Sichuan Basin were predicted to shrink under global warming. In addition, the cpDNA data revealed further divergence of the eastern lineage compared to nuclear DNA, suggesting that pollen flow is more influential than seed flow in shaping genetic structure.
In summary, this study underscores the importance of considering both seed and pollen-mediated gene flows in understanding the phylogeographic patterns of wind-pollinated relict species, highlighting the role of historical climate changes and geographical barriers in shaping current genetic distributions. The findings emphasize the need for conservation efforts focused on both exsitu and in situ strategies to protect this vulnerable species amidst environmental changes and human activities.
1.Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
2.College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
3.Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
4.Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Naypyidaw 05282, Myanmar
5.College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
6.Department of Biology and Botanic Garden, University of Fribourg, Fribourg 1700, Switzerland
7.Natural History Museum Fribourg, Fribourg 1700, Switzerland
About Yi-Gang Song
Yi-Gang Song finished his PhD at the University of Fribourg (Department of Biology) and is now developing his research group at the Chenshan Plant Science Research Center of the Chinese Academy of Sciences in Shanghai, China. His main research interests are phylogeny, phylogeography and conservation biogeography of the genus Quercus (Fagaceae) and the genus Pterocarya (Juglandaceae). In the framework of the project Zelkova he is a tree expert and coordinator of the field work in China.
Phylogeography of Pterocarya hupehensis reveals the evolutionary patterns of a Cenozoic relict tree around the Sichuan Basin
Breeding more resilient soybeans may come down to test site selection
UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES
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MAPS FROM THE UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN STUDY SUGGEST OPTIMAL TESTING SITES BASED ON AGROECOLOGICAL ZONES (AEZS) AND SOYBEAN MATURITY GROUPS (00 TO IV+).
URBANA, Ill. — In the quest to optimize crop productivity across environments, soybean breeders test new cultivars in multiple locations each year. The best-performing cultivars across these locations are selected for further breeding and eventual commercialization. However, a new study from the University of Illinois Urbana-Champaign suggests current soybean testing locations may not be delivering breeders the biggest bang for their buck.
“We met with most of the soybean breeders in public research universities across the Midwest and asked where they set up their trials over the last 30 to 40 years,” said Nicolas Martin, an associate professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at Illinois. “We found that they tend to select these sites a little bit by tradition.”
Convenience is a strong draw, as well.
“Certain types of sites are overrepresented because of tradition rather than their environmental utility; for example, sites near large research universities like Urbana, Illinois; Ames, Iowa; or Lafayette, Indiana. It’s not that we need a lot of data from those environments, but those test sites are convenient to access where cultivars are being developed,” said doctoral student Catherine Gilbert, the study’s first author.
The team analyzed long-term climate data and records of soybean trials to develop two new sets of maps that would help breeders strategize the placement and use of test sites. The first map represents common environments and favors generalist phenotypes that do well under most conditions. The second emphasizes environmental variation, optimizing specialized phenotypes that perform well in specific conditions.
“Breeding programs may have different philosophies,” Martin said. “One of them is to mimic where most farmers are growing. Others are looking to avoid redundancies in the locations where you train your cultivars. If you put them under diverse growing conditions, you see which ones are more resilient.”
In both cases, the analysis suggests breeders need to redistribute testing sites. Gilbert says there would need to be some fairly radical changes, including fully opening and closing test sites and dropping and adding hundreds of soybean varieties across the map.
“To optimize testing for general adaptation, we should expand in southern Minnesota, Iowa, and eastern South Dakota,” she said. “And for specialized adaptation, we need to put more testing sites in Nebraska and, again, in South Dakota.
When Martin and Gilbert presented their results to cooperating breeders, most said they would consider the information in decisions around moving, opening, or closing testing sites.
Basing testing networks on how well they represent the soybean growing environment, rather than on tradition or convenience, means the new maps can better account for a changing climate. The researchers hope their approach can help breeding programs select more resilient cultivars in the future.
“We think our results could guide future cultivar adaptation to growing conditions farmers are running into more frequently. Thus, our goal is to improve the environmental representation of the trials, which would let us more accurately evaluate cultivars based on their performance and select better-performing varieties,” Gilbert said.
Martin added, “The proposed site selection protocol not only enhances the accuracy of our cultivar testing but also opens doors to new regions exploring soybean cultivar adaptation. By allocating new resources in underrepresented areas that hold potential for soybean cultivar resilience, we can foster a proactive stance in cultivar development.”
The study, “Using agro-ecological zones to improve the representation of a multi-environment trial of soybean varieties,” is published in Frontiers in Plant Science [DOI:10.3389/fpls.2024.1310461].
Unlocking the secrets of black raspberry resilience: genome-wide discovery and analysis of bZIP transcription factors
MAXIMUM ACADEMIC PRESS
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MOLECULAR WEIGHT AND PROTEIN ISOELECTRIC POINT OF THE IDENTIFIED BZIPS IN EACH GROUP OF RUBUS SPECIES. ARABIDOPSIS PROTEINS ARE INCLUDED AS A REFERENCE.
Transcription factors (TFs) like basic leucine zippers (bZIPs) play vital roles in various plant biological regulation, including stress responses. However, their presence in the Rubus species has received limited attention, especially regarding the function and interactions of bZIP groups S1 and C in the Rubus genus. The current challenge lies in deepening our knowledge of these bZIP networks in non-model plants, which could inform breeding strategies and improve crop resilience.
In this study, researchers combined protein signature files from the Pfam database and a plant-specific Hidden Markov Model (HMM) to identify bZIP members. As a result, 49 candidate bZIP coding genes in both black and red raspberries were identified. These genes were confirmed to encode proteins with characteristic Basic Region (BR) and Leucine Zipper (LZ) domains, varying in length from 137 to 706 amino acids and molecular weights from 15.9 to 76.3 kDa. Phylogenetic analysis classified these into 13 phylogenetic clades, revealing interspecies clustering and suggesting an evolutionary conservation pre-dating species divergence. Additionally, genome-wide analyses revealed significant expansions or contractions in gene families, with gene duplication, especially dispersed and segmental duplications, playing a crucial role in the evolution of bZIP genes in Rubus. Comparative genomic analyses among ten Rosaceae species demonstrated a closer evolutionary relationship among roses, raspberries, and strawberries, and identified the Rubus genome as undergoing chromosomal rearrangements like those in wild strawberries.
Gene ontology annotation and expression analysis of RobZIP genes across different tissues highlighted their involvement in a wide array of cellular processes, including nitrogen metabolism and stress responses. The study also delved into the dimerization properties of the identified bZIPs, predicting potential protein interactions and validating them through yeast two-hybrid assays. Overall, this research not only provided insights into the functional redundancy and specific roles of bZIP TFs in Rubus but also underlined the evolutionary dynamics shaping their diversity across the Rosaceae family. Overall, likely due to stringent selection criteria, this research offers a foundational understanding of the bZIP gene family's contribution to the regulatory networks within and beyond the Rubus genus, paving the way for future studies on their functional mechanisms and interactions.
1College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
2College of Horticulture, Nanjing Agricultural University, Nanjing 210014, China
3University Bordeaux, INRAe, Biologie du Fruit et Pathologie, UMR 1332, av. Edouard Bourlaux, Villenave d’Ornon 33140, France
4Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China
*Corresponding author
About Qing Chen
Professor, College of Horticulture, Sichuan Agricultural University. His main research interests are in horticultural plant genetic breeding, with raspberries and strawberries as the research targets, focusing on fruit flavonoid metabolism, sugar synthesis (concentrating on the relationship with pigment synthesis in flavonoids) as well as the biosynthesis of fruit cuticle and the relationship between structure and function of the cell wall.
Heterodimeric interaction of the C/S1 basic leucine zipper transcription factors in black raspberry: a genome-wide identification and comparative analysis
Optimizing apple production: the interplay of crop load, rootstock, and chemical thinning on 'fuji' apples
MAXIMUM ACADEMIC PRESS
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EFFECT OF DIFFERENT CROP LOAD ON THE DEVELOPMENT OF TREE AND LEAVES.
Apple (Malus × domestica) is globally valued for its taste and nutrition, yet achieving optimal quality is challenging due to the impact of factors like crop load and rootstock on fruit development. Current research focuses on the individual effects of these factors and the use of chemical thinning to manage crop load, improving fruit quality and tree health. However, the complexities of chemical thinning's effects on apple physiology and its interaction with rootstock and crop load dynamics are not fully understood. Identifying the optimal use of thinning agents and their impacts on apple development is essential for refining orchard management practices and enhancing apple production outcomes.
To determine the optimal crop load for sustainable apple production across different rootstock types (vigorous, dwarfing, and dwarfing interstock), researchers adjusted crop loads to various levels and assessed the effects on tree growth and fruit quality. A crop load of 320 fruits per tree for vigorous rootstocks resulted in optimal tree height growth and branch diameter. Dwarfing rootstocks showed the best results with a crop load of 110 fruits, although the length of new branch growth was not significantly affected. Dwarfing interstock trees had optimal growth with a crop load of 210 fruits. Increased crop load in vigorous rootstocks also enhanced leaf area, chlorophyll content, and photosynthetic rates, suggesting a positive correlation between crop load and leaf functionality, unlike in dwarfing rootstocks where an optimal balance was needed to maintain leaf health and photosynthetic efficiency.
Fruit quality, assessed through weight, yield, and size, generally decreased with increasing crop load, but yield per acre increased. The study recommended specific crop loads for each rootstock type to balance tree health and fruit quality: 320 fruits for vigorous stock, 90 for dwarfing rootstock, and 100 for dwarfing interstock for quality fruits exceeding 80 mm in diameter. Chemical thinning, using carbaryl and 6-BA, was identified as effective in achieving optimal crop loads, with best practices involving specific concentrations and application timings.
Additionally, transcriptomic analysis of NAA-treated fruits revealed its inhibitory effect on fruit enlargement and identified potential regulatory genes involved in hormonal pathways affecting fruit development and ripening. Overall, this approach combining practical orchard management practices with molecular insights offers a pathway to enhancing apple production efficiency and fruit quality, recommending specific crop loads and thinning practices tailored to different rootstock types while elucidating the role of NAA in fruit development processes.
# These authors contributed equally: Shicong Wang, Qianying Wang
Affiliations
1. State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
2. Institute of Pomology Science, Guizhou Academy of Agricultural Science, Guiyang 550006, China
3.The National and Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology of Characteristic Fruit Trees in Southern Xinjiang, College of Horticulture and Forestry, Tarim University, Alar 843300, China
4. Xinjiang Production and Construction Corps Key Laboratory of Biological Resources Protection and Utilization in Tarim Basin, Alar 843300, China
# These authors contributed equally.
About Jidi Xu
Associate Professor, College of Horticulture, Northwest A&F University. His group aims to investigate the underlying mechanism of epigenetic regulation in apples under various abiotic stresses, including DNA/RNA modification, histone modification, and chromatin remodeling. Based on the mechanism exploring, epigenome editing engineering is applied to process the important traits improvement in apples.
Evaluating the sustainable cultivation of 'Fuji' apples: suitable crop load and the impact of chemical thinning agents on fruit quality and transcription
