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AI model learns yeast DNA ‘language’ to boost protein drug output

Industrial yeasts are a powerhouse of protein production, used to manufacture vaccines, biopharmaceuticals, and other useful compounds. In a new study, MIT chemical engineers have harnessed artificial intelligence to optimize the development of new protein manufacturing processes, which could reduce the overall costs of developing and manufacturing these drugs.

Using a large language model (LLM), the MIT team analyzed the genetic code of the industrial yeast Komagataella phaffii—specifically, the codons that it uses. There are multiple possible codons, or three-letter DNA sequences, that can be used to encode a particular amino acid, and the patterns of codon usage are different for every organism.

The new MIT model learned those patterns for K. phaffii and then used them to predict which codons would work best for manufacturing a given protein. This allowed the researchers to boost the efficiency of the yeast’s production of six different proteins, including human growth hormone and a monoclonal antibody used to treat cancer.

A potential new lymphedema target: Clearing cholesterol deposits to reduce swelling

An international team led by National University of Singapore researchers has linked secondary lymphedema to excessive cholesterol buildup inside skin and around lymphatic vessels. Excess cholesterol deposition tracked with dermal fat cell enlargement, fat cell dysfunction, cell death, and fibrosis, while cholesterol-clearing interventions reduced swelling and improved lymphatic drainage in mouse models, alongside reduced tissue cholesterol and clinical procedures that improved drainage.

Secondary lymphedema involves impaired lymphatic drainage with progressive swelling, fat expansion, inflammation, and fibrosis, often following cancer treatment, infection, or injury. Lymphatic vessels transport cholesterol from peripheral tissues back into circulation, placing cholesterol clearance inside the functional scope of normal lymphatic drainage. Lymphatic vessels also have roles in immune surveillance, tissue fluid balance, and lipid transport.

In the study, “Targeting excessive cholesterol deposition alleviates secondary lymphoedema,” published in Nature, researchers investigated whether lymphatic insufficiency alters cholesterol handling and adipose tissue architecture.

Earlier immunotherapy is spreading in cancer care: Who benefits and what are the risks?

Immunotherapy given before or after surgery is increasingly used across several cancer areas. In an article published in the Journal of Internal Medicine, researchers at Karolinska Institutet present a comprehensive review of studies across seven tumor areas, showing how the field is moving toward earlier treatment.

For several years, immunotherapy has transformed the treatment of advanced cancer that can no longer be removed surgically. It is now used more frequently in earlier stages of disease as well—before surgery, known as neoadjuvant treatment, or after surgery, known as adjuvant treatment.

In the new article, the researchers summarize findings from studies on several cancer diagnoses, grouped into seven tumor areas: skin cancer, lung cancer, breast cancer, gastrointestinal cancer, gynecological cancer, head and neck cancer, and urological cancer.

The Deflationary Singularity: Why Everything is Going to ZERO w/ Salim Ismail

The rapid advancement of technologies, particularly AI, is driving the world towards an economic singularity where the marginal cost of essentials approaches zero, leading to a deflationary future and a potential transformation of traditional systems and societies ##

## Questions to inspire discussion.

Education Transformation.

🎓 Q: How will AI reduce education time while improving effectiveness?

A: AI will customize education to each child’s learning style, reducing daily learning time to 1 hour per day while delivering 5 times more effective learning compared to traditional methods, with costs falling to zero within 3–5 years and breaking the university industry that currently creates massive student debt.

Healthcare Revolution.

Molecular ‘knitting machine’ for bacterial capsules mapped in 3D

Most bacteria, including many bacterial pathogens, are surrounded by an outer protective layer of sugar molecules, known as a capsule. This primarily protects the bacteria from environmental influences, but also serves as a kind of cloak of invisibility, enabling them to evade the phagocytes of our immune system. Structural biologists at the Helmholtz Center for Infection Research (HZI) have now used cryo-electron microscopy to visualize the central Wza-Wzc protein complex, with which sugar molecules pass from the interior of the bacterial cell to the outside, in three dimensions at the atomic level for the first time.

Their investigations also show how the channel is formed and which molecular players are involved in the active transport of sugar molecules through the channel. The researchers hope that their study will help identify target structures for potential drugs that could inhibit or completely prevent the formation of the bacterial capsule in the future. This would also make such bacterial pathogens vulnerable to attack by the immune system.

The study was conducted in collaboration with researchers from the Center for Structural Systems Biology (CSSB) in Hamburg and has now been published in the journal Nature Communications.

Peripheral Neural Plasticity in Cochlear Implant Users Across the Lifespan

Model-based analysis of ECAPs in CochlearImplant users showed stronger auditory nerve responses and plasticity in younger recipients, highlighting the value of early implantation.


Question Can neural responses measured in cochlear implant users be standardized to monitor auditory nerve health and plasticity over time?

Findings In this cohort study analyzing more than 169 000 recordings from more than 10 000 cochlear implants in 7,416 patients, auditory nerve activity varied by cochlear location and age at implantation. Children implanted at younger ages showed stronger responses and clear evidence of plasticity, particularly in the first 5 years after activation; these changes were not observed in older users.

Meaning Model-based analysis of neural recordings provide a scalable method for tracking auditory nerve health across the lifespan and highlight the importance of early implantation for long-term outcomes.

Ancestry-Associated Performance Variability of Open-Source AI Models for EGFR Prediction in Lung Cancer

Open-source AI models for LungCancer EGFR mutation prediction showed high accuracy overall but reduced performance in Asian patients and pleural samples, indicating the need for broader validation.


Importance Artificial intelligence (AI) models are emerging as rapid, low-cost tools for predicting targetable genomic alterations directly from routine pathology slides. Although these approaches could accelerate treatment decisions in lung cancer, little is known about whether their performance is consistent across diverse patient populations and tissue contexts.

Objective To evaluate the performance and generalizability of 2 open-source AI pathology models for predicting EGFR mutation status in lung adenocarcinoma (LUAD) across independent cohorts and ancestral subgroups.

Design, Setting, and Participants This cohort study included patients with LUAD from 2 cohorts: Dana-Farber Cancer Institute (DFCI) from June 2013 to November 2023, and a European-based trial (TNM-I) from August 2016 to February 2022. All patients had paired next-generation sequencing data and hematoxylin-eosin–stained whole-slide images. In the DFCI cohort, genetic ancestry was inferred using germline genotype data. Data analyses were performed from July 2025 to September 2025.

Researchers uncover MraZ ‘donut’ deformation that triggers bacterial cell division

A research team led by UAB researcher David Reverter has discovered the molecular mechanism that describes in detail the process regulating cell division in bacteria, based on the binding of the MraZ protein to the dcw gene cluster. The research has been published in Nature Communications.

Cell division is a central process in all living organisms and requires the coordinated action of many proteins and other regulatory elements. In most bacteria, this process is encoded in a gene cluster called the dcw operon, which groups all the genes that produce the proteins necessary to carry out cell division and bacterial wall formation.

These sets of genes are activated by proteins that act as transcription factors: they bind to the promoter region of the gene, the DNA sequence that indicates the point to start transcription, just before the first codon (the basic unit of gene information) that codes for the beginning of the protein sequence. One of these transcription factors is MraZ, the first gene of the dcw operon in all bacteria. When activated, the necessary proteins (encoded within the genes of the operon) are produced so that the bacteria can divide. It is, therefore, the transcription factor that controls the activity of the operon responsible for cell division in most bacteria.

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