Simulating cancer genomes Yevgeniya Nusinovich
Most studies of cancer genomics analyze existing tumors, probing their genetic sequence for clues as to what mutations drive their initiation and progression. However, this approach requires access to patient materials, so it presents privacy issues and may be limited by the availability of tumors with specific mutation patterns. As an alternative, Díaz-Navarro et al. used generative AI trained on databases of existing cancer genomes to create synthetic ones that mimic real tumors. It remains to be seen whether these synthetic cancer genomes can help to uncover new tumor biology, and there are some types of genetic damage that they cannot replicate yet, but this orthogonal approach may yield biological insights. Synthetic Biology Exploring multicellularity with yeast L. Bryan Ray Yeast lack the specific adhesion interactions and cell contact–dependent signals that allow more complex processes in multicellular organisms. With an eye to enabling synthetic biology applications, Meng et al. explored whether yeast cells could be programmed to exhibit multicellular behaviors. They engineered Saccharomyces cerevisiae cells to express surface proteins that mediate signaling between cells that come into physical contact. The toolkits that they developed allowed control of cell adhesion and consequent signaling between cells to create multicellular logic circuits that recapitulate cellular interactions in the development of multicellular organisms. The authors designed a sensor for protein-protein interactions and anticipate other applications in biotechnology. Ancient DNA from cave sediments gives a rare glimpse of Norwegian coastal fauna before the Last Glacial Maximum. Although deep-time paleogenomic studies have increased in recent years, preserving organic remains requires specific circumstances. Glacier melting and erosion can disperse organic material, leaving behind only rock. Walker et al. performed stratigraphic analysis in a cave in northern Norway with geomorphological features that allowed for draining of glacial meltwater without sediment layer disruption. These sediments predate the Last Glacial Maximum and are likely about 71,000 to 85,000 years old. Bulk-bone metabarcoding revealed DNA from 46 animal taxa encompassing birds, mammals, and fish, as well as pollen and marine invertebrates. These data grant a previously unseen snapshot of this Arctic coastal environment, including the identification of a now extinct species that has been rarely documented. Little red dots (LRDs) are a class of distant galaxies that are compact, red, and lack x-ray emission. Their physical nature is debated, but one possibility is that they are active galaxies with the supermassive black hole (SMBH) in their nuclei obscured by surrounding gas. Taylor et al. observed an LRD at redshift 9.2, about 500 million years after the Big Bang. Spectral line analysis showed that it contains a surprisingly massive SMBH, over 5% of the stellar mass of the galaxy, and is seemingly surrounded by very dense gas. It remains unclear how such a massive SMBH could have formed so early or how the high gas density could be maintained. Self-assembled islands of C60 on graphene create well-defined hole-doped regions that act as mid-infrared plasmonic cavities. Rizzo et al. thermally evaporated C60 onto graphene to form clusters ranging from 50 to 300 nanometers in diameter. Scattering-type scanning near-field optical microscopy revealed high-contrast surface plasmon polariton cavity modes, as verified by energy-dependent measurements and optical modeling. The surface plasmon polariton wavelength could be tuned by altering the deposition conditions to change the cluster sizes. During the pathogenesis of Alzheimer’s disease, some neurons become pathologically hyperactive, whereas others turn silent. Although neuronal hyperactivity has been extensively studied, Zhang et al. investigated the mechanisms underlying neurons becoming virtually silent in Alzheimer’s disease. Combining awake two-photon imaging, single-neuron intracellular recordings, and single-neuron trans-synaptic tracing followed by post-mortem large-scale imaging of presynaptic neurons, the authors identified hyperactive or silent cells in vivo, recorded their subthreshold firing patterns, and conducted post-mortem tracing of the neuron’s presynaptic inputs. Silent neurons showed a profound loss of both excitatory and inhibitory inputs compared with hyperactive neurons, which exhibited surprisingly few changes. This synaptic decoupling may play an important role in the earliest stages of Alzheimer’s disease. Student evaluations of teaching are gender biased, and interventions for mitigating these biases are being studied. Mitchem et al. investigated whether the introduction of a simple AntiBias statement to student evaluations could mitigate bias toward instructor gender within the context of a biology department. Over the course of three semesters, students were given either the original evaluation or one containing the AntiBias text. Results were mixed, with the AntiBias treatment inconsistently influencing student evaluations. Qualitative analysis revealed that the students’ comments were mostly not affected by the conditions of treatment or instructor gender, although students receiving the AntiBias treatment wrote more. These results suggest that mitigating gender bias in teaching evaluations is nuanced and will likely not result from a simple intervention. CBE Life Sci. Educ. (2025) 10. K Rajaram IRS 31025 -- You received this message because you are subscribed to the Google Groups "Thatha_Patty" group. 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