Unconventional roles of nonlipidated LC3 in ERAD tuning and coronavirus infection

Secretory and membrane proteins attain their native structure in the endoplasmic reticulum (ER). Folding-defective polypeptides are selected for degradation by processes collectively defined as ER-associated degradation (ERAD). Enhanced ERAD activity may interfere with protein biogenesis by inappropriately targeting not-yet-native protein folding intermediates for disposal. The regulation of ERAD is therefore crucial to maintain cellular proteostasis. At steady-state, select ERAD regulators are constitutively removed from the ER in a series of processes collectively defined as ERAD tuning. This sets the ERAD activity at levels that do not interfere with completion of ongoing folding programs. Our latest work highlights a crucial, autophagy-independent role of nonlipidated LC3 (LC3-I) as part of a membrane-bound receptor that insures the vesicle-mediated clearance of at least two ERAD regulators from the ER, EDEM1 and OS9. This pathway is hijacked by coronaviruses (CoV), and silencing of LC3 substantially inhibits viral replication.     

Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.     

Contribution of GABAA receptor-mediated inhibition to the determination of the velocity tuning of low pass-tuned neurons of the Superior Colliculus

The participation of intrinsic inhibitory networks in providing the velocity selectivity of neurons of the superior colliculus (SC) of the Syrian hamster was tested using iontophoretic application of bicuculline methiodide, a GABA_A receptor competitive antagonist. The impulse activity of 22 low pass-tuned (LP) cells was recorded extracellularly. Following application of bicuculline, 10 cells exhibited an increase in the velocity selectivity, while the other 12 units showed decreases in their tuning. We assume that SC intrinsic inhibitory networks contributing to the velocity tuning of neurons of this structure are driven in a dissimilar way by afferent volleys arriving from the retina through “fast” Y and “slow” W channels. Neirofiziologiya/Neurophysiology, Vol. 39, Nos. 4/5, pp. 385–387, July–October, 2007.     

Listening for males and bats: spectral processing in the hearing organ of <Emphasis Type="Italic">Neoconocephalus bivocatus</Emphasis> (Orthoptera: Tettigoniidae)

Tettigoniids use hearing for mate finding and the avoidance of predators (mainly bats). Using intracellular recordings, we studied the response properties of auditory receptor cells of Neoconocephalus bivocatus to different sound frequencies, with a special focus on the frequency ranges representative of male calls and bat cries. We found several response properties that may represent adaptations for hearing in both contexts. Receptor cells with characteristic frequencies close to the dominant frequency of the communication signal were more broadly tuned, thus extending their range of high sensitivity. This increases the number of cells responding to the dominant frequency of the male call at low signal amplitudes, which should improve long distance call localization. Many cells tuned to audio frequencies had intermediate thresholds for ultrasound. As a consequence, a large number of receptors should be recruited at intermediate amplitudes of bat cries. This collective response of many receptors may function to emphasize predator information in the sensory system, and correlates with the amplitude range at which ultrasound elicits evasive behavior in tettigoniids. We compare our results with spectral processing in crickets, and discuss that both groups evolved different adaptations for the perceptual tasks of mate and predator detection.     

弱噪声对小鼠下丘神经元频率调谐的影响

为探讨弱噪声对小鼠 (MusmusculusKm)中脑下丘 (inferiorcolliculus ,IC)神经元声信号提取的影响 ,采用单位胞外记录方法 ,研究了加入弱白噪声 (强度相当于纯音阈强度下 5dB)前后神经元频率调谐曲线的变化。实验共记录到 10 4个下丘神经元 ,测量了 32个神经元的频率调谐曲线。结果显示 :①弱噪声条件下神经元的频率调谐曲线表现出 3种类型 ,即锐化 (34 4 % ,11/ 32 )、拓宽 (18 8% ,6 / 32 )和不受影响 (4 6 9% ,15 / 32 ) ,其中锐化呈现有意义的变化 ;②频率调谐受弱噪声锐化的神经元 ,其Q10 、Q3 0 平均分别增大 (34 4 2±17 0 4 ) % (P =0 0 2 6 ,n =11)和 (4 6 34± 2 2 88) % (P =0 0 0 9,n =7) ,且Q3 0 变化率大于Q10 ;③弱噪声对调谐曲线的高、低频边锐化度不一 ,神经元低频边的反转斜率基本不变 [由 0 16± 0 0 8变为 0 16± 0 0 7kHz/dB (P =0 94 7,n =7) ],而高频边明显下降 [由 0 5 2± 0 2 5下降为 0 2 6± 0 13kHz/dB ,平均减小 (4 3 81±2 4 0 6 ) % ,(P =0 0 4 6 ,n =7) ]。上述结果表明 ,弱噪声可锐化小鼠IC神经元频率调谐 ,并强化神经元的声信号高频分析能力     

Systematic optimization of L‐tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli

Riboswitches form a class of genetically encoded sensor‐regulators and are considered as promising tools for monitoring various metabolites. Functional parameters of a riboswitch, like dynamic or operational range, should be optimized before the riboswitch is implemented in a specific application for monitoring the target molecule efficiently. However, optimization of a riboswitch was not straightforward and required detailed studies owing to its complex sequence‐function relationship. Here, we present three approaches for tuning and optimization of functional parameters of a riboswitch using an artificial L‐tryptophan riboswitch as an example. First, the constitutive expression level was adjusted to control the dynamic range of an L‐tryptophan riboswitch. The dynamic range increased as the constitutive expression level increased. Then, the function of a riboswitch‐encoded protein was utilized to connect the regulatory response of the riboswitch to another outcome for amplifying the dynamic range. Riboswitch‐mediated control of the host cell growth enabled the amplification of the riboswitch response. Finally, L‐tryptophan aptamers with different dissociation constants were employed to alter the operational range of the riboswitch. The dose‐response curve was shifted towards higher L‐tryptophan concentrations when an aptamer with higher dissociation constant was employed. All strategies were effective in modifying the distinct functional parameters of the L‐tryptophan riboswitch, and they could be easily applied to optimization of other riboswitches owing to their simplicity.     

Computational Modeling of Orientation Tuning Dynamics in Monkey Primary Visual Cortex

In the primate visual pathway, orientation tuning of neurons is first observed in the primary visual cortex. The LGN cells that comprise the thalamic input to V1 are not orientation tuned, but some V1 neurons are quite selective. Two main classes of theoretical models have been offered to explain orientation selectivity: feedforward models, in which inputs from spatially aligned LGN cells are summed together by one cortical neuron; and feedback models, in which an initial weak orientation bias due to convergent LGN input is sharpened and amplified by intracortical feedback. Recent data on the dynamics of orientation tuning, obtained by a cross-correlation technique, may help to distinguish between these classes of models. To test this possibility, we simulated the measurement of orientation tuning dynamics on various receptive field models, including a simple Hubel-Wiesel type feedforward model: a linear spatiotemporal filter followed by an integrate-and-fire spike generator. The computational study reveals that simple feedforward models may account for some aspects of the experimental data but fail to explain many salient features of orientation tuning dynamics in V1 cells. A simple feedback model of interacting cells is also considered. This model is successful in explaining the appearance of Mexican-hat orientation profiles, but other features of the data continue to be unexplained.     

On the use of cross-validation for the calibration of the adaptive lasso

Cross-validation is the standard method for hyperparameter tuning, or calibration, of machine learning algorithms. The adaptive lasso is a popular class of penalized approaches based on weighted L₁-norm penalties, with weights derived from an initial estimate of the model parameter. Although it violates the paramount principle of cross-validation, according to which no information from the hold-out test set should be used when constructing the model on the training set, a “naive” cross-validation scheme is often implemented for the calibration of the adaptive lasso. The unsuitability of this naive cross-validation scheme in this context has not been well documented in the literature. In this work, we recall why the naive scheme is theoretically unsuitable and how proper cross-validation should be implemented in this particular context. Using both synthetic and real-world examples and considering several versions of the adaptive lasso, we illustrate the flaws of the naive scheme in practice. In particular, we show that it can lead to the selection of adaptive lasso estimates that perform substantially worse than those selected via a proper scheme in terms of both support recovery and prediction error. In other words, our results show that the theoretical unsuitability of the naive scheme translates into suboptimality in practice, and call for abandoning it.     

Rod opsin sequence in the John Dory: further evidence for the spectral tuning of rhodopsin

The opsin from the John Dory Zeus faber rod visual pigment (maximum spectral sensitivity =492 nm) was cloned and sequenced. Comparison of the John Dory rod opsin sequence with those from other fish with blue-shifted scotopic spectral sensitivity provides further evidence for the spectral tuning of this group of visual pigments.