Active learning of enhancers and silencers in the developing neural retina.

Deep learning is a promising strategy for modeling cis-regulatory elements. However, models trained on genomic sequences often fail to explain why the same transcription factor can activate or repress transcription in different contexts. To address this limitation, we developed an active learning approach to train models that distinguish between enhancers and silencers composed of binding sites for the photoreceptor transcription factor cone-rod homeobox (CRX).

Discretized representations in V1 predict suboptimal orientation discrimination.

Neuronal population activity in sensory cortices is the substrate for perceptual decisions. Yet, we still do not understand how neuronal information content in sensory cortices relates to behavioral reports. To reconcile neurometric and psychometric performance, we recorded the activity of V1 neurons in mice performing a Go/NoGo orientation discrimination task.

represses short-wavelength cone genes to preserve long-wavelength cone and rod photoreceptor identity.

The role of transcription factors in photoreceptor gene regulation is fairly well understood, but knowledge of the cell-type-specific function of transcriptional cofactors remains incomplete. Here, we show that the transcriptional corepressor promotes rod differentiation and represses short-wavelength cone genes in long-wavelength cones in zebrafish. In retinas, red cones are transformed into hybrid red/ultraviolet (UV) cones, green cones are absent, the number of blue cones is approximately doubled, and the number of rods is greatly reduced.

A molecular mechanism for bright color variation in parrots.

Parrots produce stunning plumage colors through unique pigments called psittacofulvins. However, the mechanism underlying their ability to generate a spectrum of vibrant yellows, reds, and greens remains enigmatic. We uncover a unifying chemical basis for a wide range of parrot plumage colors, which result from the selective deposition of red aldehyde- and yellow carboxyl-containing psittacofulvin molecules in developing feathers.

Mechanisms of lipid droplet degradation.

Lipid droplets (LDs) are subcellular organelles that play an integral role in lipid metabolism by regulating the storage and release of fatty acids, which are essential for energy production and various cellular processes. Lipolysis and lipophagy are the two major LD degradation pathways that mediate the utilization of lipids stored in these organelles. Recent studies have further uncovered alternative pathways, including direct lysosomal LD degradation and LD exocytosis.