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Category: genetics

Qualia as Structured Silence: Colour Opponency via Dual-Regime Refusal

By: Alastair Waterman https://www.facebook.com/share/p/1N1TBvEKuF/

Why does red feel exactly like red, green exactly like green, and why can these two experiences never, ever swap places?

Most current theories of consciousness have no real answer. They explain how the brain detects wavelength, but not why one neural pattern feels “red” and its literal opponent feels “green”

Refusal-Driven Dimensionality Reduction Theory (RDRT) offers the first direct mechanism.

Colour vision is opponent at every level: red and green are mutually exclusive from retina → LGN → V1 → V4 → inferotemporal cortex.

This hard-wired mutual exclusion is a multi-level structural refusal.

The claim: The specific feeling of redness is not the spikes that are transmitted.

It is the precise, reproducible shape of what is refused transmission — a stable ~55–65-event “hole” carved into each gamma cycle in the anterior cingulate cortex and self-monitoring networks.

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Enduring patterns in world’s languages: One-third of grammatical ‘universals’ stand up to rigorous testing

Despite the vast diversity of human languages, specific grammatical patterns appear again and again. A new study reveals that around a third of the long-proposed “linguistic universals”—patterns thought to hold across all languages—are statistically supported when examined with state-of-the-art evolutionary methods.

An international team led by Annemarie Verkerk (Saarland University) and Russell D. Gray (Max Planck Institute for Evolutionary Anthropology) used Grambank, the world’s most comprehensive database of grammatical features, to test 191 proposed universals across more than 1,700 languages. Traditionally, linguists have attempted to circumvent the genealogical and geographic non-independence of languages by sampling widely separated languages.

However, sampling can fail to remove all dependencies, reduce statistical power and does not identify historical pathways. The Bayesian spatio-phylogenetic analyses used by the authors accounted for both the genealogical and geographic non-independence of languages—a level of statistical rigor rarely achieved in previous work.

Shock Discovery Reveals Sea Urchins Are Basically ‘All Brain’

Sea urchins may just look like a ball of spikes waiting to be stepped on at the tide pool, but there’s much more to these barbed beasts than just roe and teeth.

New research reveals sea urchin nervous systems are far more complex than we knew. These creatures, it turns out, possess ‘all-body brains’ and, at least in their genetic layout, they are remarkably similar to our own.

A team of scientists led by developmental biologist Periklis Paganos from Stazione Zoologica Anton Dohrn in Italy made the discovery while investigating metamorphosis in purple sea urchins (Paracentrotus lividus), which transform from free-swimming, planktonic larvae to the mature, spine-encrusted form we’re more familiar with.

Strange Structures Found Lurking in The Blood of People With Long COVID

A hidden physical change in the body may be helping to drive the prolonged malaise some people experience after contracting COVID-19.

Analyzing blood samples from patients with long COVID, a team of medical researchers has identified unusual microscopic structures that may contribute to symptoms such as brain fog and fatigue. If this is the case, it offers a hopeful target for future treatment.

“This study shows a robust association between biomarkers indicative of thromboinflammatory activity and long COVID,” the team writes in a paper led by geneticist Alain Thierry of Montpellier University in France.

Advancing Drug Discovery with Artificial Intelligence

Lipid nanoparticles (LNPs) have emerged as popular vehicles for delivering various types of drugs such as mRNA and gene therapy. While these nanoparticles are effective in transporting therapeutic payloads, their components can interact with the human body, potentially causing genotoxicity — damage to the recipient’s genetic material that may lead to inheritable mutations or cancer. In this webinar brought to you by Inotiv, Shambhu Roy will discuss how to test the genotoxicity of LNP-based therapeutics to ensure the safety of these innovative drug delivery systems.

We’ll chat about these topics.

• Understanding the key components of LNP delivery systems • Genotoxicity testing for LNP-based drugs during preclinical safety assessment • Selecting the appropriate assays to meet regulatory requirements.

Fibromyalgia: A Review of the Pathophysiological Mechanisms and Multidisciplinary Treatment Strategies

Fibromyalgia is a syndrome characterized by chronic widespread musculoskeletal pain, which may or may not be associated with muscle or joint stiffness, accompanied by other symptoms such as fatigue, sleep disturbances, anxiety, and depression. It is a highly prevalent condition globally, being considered the third most common musculoskeletal disorder, following lower back pain and osteoarthritis. It is more prevalent in women than in men, and although it can occur at any age, it is more common between the ages of thirty and thirty-five. Although the pathophysiology and etiopathogenesis remain largely unknown, three underlying processes in fibromyalgia have been investigated. These include central sensitization, associated with an increase in the release of both excitatory and inhibitory neurotransmitters; peripheral sensitization, involving alterations in peripheral nociceptor signaling; and inflammatory and immune mechanisms that develop concurrently with the aforementioned processes. Furthermore, it has been determined that genetic, endocrine, psychological, and sleep disorders may influence the development of this pathology. The accurate diagnosis of fibromyalgia remains challenging as it lacks specific diagnostic biomarkers, which are still under investigation. Nonetheless, diagnostic approaches to the condition have evolved based on the use of scales and questionnaires for pain identification. The complexity associated with this pathology makes it difficult to establish a single effective treatment. Therefore, treatment is multidisciplinary, involving both pharmacological and non-pharmacological interventions aimed at alleviating symptoms. The non-pharmacological treatments outlined in this review are primarily related to physiotherapy interventions. The effectiveness of physical exercise, both on land and in water, as well as the application of electrotherapy combined with transcranial therapy and manual therapy has been highlighted. All of these interventions aim to improve the quality of life of patients highly affected by fibromyalgia.

XP140BR: 6-year-old girl with XP-J

This issue’s cover features companion papers that exemplify how understanding a rare disease can inform treatment strategies in other conditions.

Fassihi et al. and Nakazawa et al. report on the C-terminal deletion of transcription factor TFIIH-p52 subunit as a cause of xeroderma pigmentosum.

The cover art was created using PyMOL; TFIIH-p52 subunit (blue; C-terminus in white). Image credit: Keiko Itano.

https://www.jci.org/articles/view/195731 https://www.jci.org/articles/view/195732

1National Xeroderma Pigmentosum Service, Rare Disease Centre, Guy’s and St Thomas’ NHS Trust, London, United Kingdom.

2Department of Molecular Genetics, Nagoya University Graduate School of Medicine, Nagoya, Japan.

Continue reading “XP140BR: 6-year-old girl with XP-J” | >

Immunomodulatory Role of Microbiota in Inflammation and Cancer

Non-small cell lung cancer (NSCLC) is the most prevalent form of lung cancer, accounting for approximately 85% of all cases, and is associated with a poor prognosis. Despite significant advancements in treatment modalities, therapeutic efficacy remains suboptimal, underscoring the urgent need for novel strategies. In recent years, increasing attention has been directed toward the pivotal role of gut microbiota-host interactions in the treatment of NSCLC. This review systematically examines the influence of current NSCLC therapies on gut microbiota and metabolism, explores the relationship between the microbiome and therapeutic response, and highlights the critical functions of probiotics, microbial metabolites, fecal microbiota transplantation (FMT), and dietary interventions in NSCLC management. By elucidating the mechanisms through which gut microbiota and their metabolites modulate treatment efficacy, we investigate the potential of exogenous interventions targeting the gut ecosystem to enhance therapeutic outcomes and mitigate adverse effects. Modulating the intestinal microbiota represents a promising clinical avenue and offers a new frontier for the development of future NSCLC treatment strategies.

The human microbiome comprises a diverse and dynamic community of microorganisms—including bacteria, fungi, viruses—their genetic material, and metabolic byproducts. The resident microbiota is an essential component of host health and homeostasis (1). Most microbiome research to date has focused on bacterial populations, which constitute a major proportion of these resident microbes (2). In the gut, Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria dominate the bacterial composition (3– 5). The gut microbiota plays a pivotal role in regulating host immunity and metabolism through the production of numerous metabolites that function as signaling molecules and metabolic substrates, linking dysbiosis with inflammation and tumorigenesis (6– 8).

The cross-link between gut microbiota and lung cancer is a complex multifactorial relationship. Studies have shown that in patients with lung cancer, the abundance of Bacteroidetes, Fusobacteria, Cyanobacteria, and Spirochaetes increases in both pulmonary and intestinal microbiomes, while Firmicutes are significantly reduced (4, 9). Research on both gut and respiratory tract microbiota has revealed notable dysregulation in NSCLC, which is further associated with distant metastasis (DM) (10). The pathogenic contribution of the gut microbiome and its specific metabolites to NSCLC lies in their modulation of chronic inflammation and immune dysregulation (11). A study combining serum metabolomics and fecal microbiome profiling identified potential biomarkers in patients with early-stage NSCLC. The metabolomic analysis revealed elevated levels of sphingolipids (e.g. D-erythrosphingosine 1-phosphate, palmitoylsphingomyelin), fatty acyls (e.g.

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