Occam's Razor in sensorimotor learning

A large number of recent studies suggest that the sensorimotor system uses probabilistic models to predict its environment and makes inferences about unobserved variables in line with Bayesian statistics. One of the important features of Bayesian statistics is Occam''s Razor—an inbuilt preference for simpler models when comparing competing models that explain some observed data equally well. Here, we test directly for Occam''s Razor in sensorimotor control. We designed a sensorimotor task in which participants had to draw lines through clouds of noisy samples of an unobserved curve generated by one of two possible probabilistic models—a simple model with a large length scale, leading to smooth curves, and a complex model with a short length scale, leading to more wiggly curves. In training trials, participants were informed about the model that generated the stimulus so that they could learn the statistics of each model. In probe trials, participants were then exposed to ambiguous stimuli. In probe trials where the ambiguous stimulus could be fitted equally well by both models, we found that participants showed a clear preference for the simpler model. Moreover, we found that participants’ choice behaviour was quantitatively consistent with Bayesian Occam''s Razor. We also show that participants’ drawn trajectories were similar to samples from the Bayesian predictive distribution over trajectories and significantly different from two non-probabilistic heuristics. In two control experiments, we show that the preference of the simpler model cannot be simply explained by a difference in physical effort or by a preference for curve smoothness. Our results suggest that Occam''s Razor is a general behavioural principle already present during sensorimotor processing.     

TDP-43 potentiates alpha-synuclein toxicity to dopaminergic neurons in transgenic mice

TDP-43 and α-synuclein are two disease proteins involved in a wide range of neurodegenerative diseases. While TDP-43 proteinopathy is considered a pathologic hallmark of sporadic amyotrophic lateral sclerosis and frontotemporal lobe degeneration, α-synuclein is a major component of Lewy body characteristic of Parkinson's disease. Intriguingly, TDP-43 proteinopathy also coexists with Lewy body and with synucleinopathy in certain disease conditions. Here we reported the effects of TDP-43 on α-synuclein neurotoxicity in transgenic mice. Overexpression of mutant TDP-43 (M337V substitution) in mice caused early death in transgenic founders, but overexpression of normal TDP-43 only induced a moderate loss of cortical neurons in the transgenic mice at advanced ages. Interestingly, concomitant overexpression of normal TDP-43 and mutant α-synuclein caused a more severe loss of dopaminergic neurons in the double transgenic mice as compared to single-gene transgenic mice. TDP-43 potentiated α-synuclein toxicity to dopaminergic neurons in living animals. Our finding provides in vivo evidence suggesting that disease proteins such as TDP-43 and α-synuclein may play a synergistic role in disease induction in neurodegenerative diseases.     

Presenilin 1 controls gamma-secretase processing of amyloid precursor protein in pre-golgi compartments of hippocampal neurons.

Mutations of presenilin 1 (PS1) causing Alzheimer's disease selectively increase the secretion of the amyloidogenic betaA4(1-42), whereas knocking out the gene results in decreased production of both betaA4(1-40) and (1-42) amyloid peptides (De Strooper et al. 1998). Therefore, PS1 function is closely linked to the gamma-secretase processing of the amyloid precursor protein (APP). Given the ongoing controversy on the subcellular localization of PS1, it remains unclear at what level of the secretory and endocytic pathways PS1 exerts its activity on APP and on the APP carboxy-terminal fragments that are the direct substrates for gamma-secretase. Therefore, we have reinvestigated the subcellular localization of endogenously expressed PS1 in neurons in vitro and in vivo using confocal microscopy and fine-tuned subcellular fractionation. We show that uncleaved PS1 holoprotein is recovered in the nuclear envelope fraction, whereas the cleaved PS fragments are found mainly in post-ER membranes including the intermediate compartment (IC). PS1 is concentrated in discrete sec23p- and p58/ERGIC-53-positive patches, suggesting its localization in subdomains involved in ER export. PS1 is not found to significant amounts beyond the cis-Golgi. Surprisingly, we found that APP carboxy-terminal fragments also coenrich in the pre-Golgi membrane fractions, consistent with the idea that these fragments are the real substrates for gamma-secretase. Functional evidence that PS1 exerts its effects on gamma-secretase processing of APP in the ER/IC was obtained using a series of APP trafficking mutants. These mutants were investigated in hippocampal neurons derived from transgenic mice expressing PS1wt or PS1 containing clinical mutations (PS1(M146L) and PS1(L286V)) at physiologically relevant levels. We demonstrate that the APP-London and PS1 mutations have additive effects on the increased secretion of betaA4(1-42) relative to betaA4(1-40), indicating that both mutations operate independently. Overall, our data clearly establish that PS1 controls gamma(42)-secretase activity in pre-Golgi compartments. We discuss models that reconcile this conclusion with the effects of PS1 deficiency on the generation of betaA4(1-40) peptide in the late biosynthetic and endocytic pathways.     

基于功能性状的外来植物入侵预测模型框架构建

预测外来植物的潜在入侵性已成为生物多样性保护研究的重要内容,外来植物与乡土物种间的亲缘关系是预测外来植物能否成功入侵的一个重要途径。然而,达尔文归化难题却预测了两种截然不同的结果(即达尔文归化假说和预适应假说)。该研究解析了达尔文归化难题的内涵,提出了基于功能性状的外来植物与乡土群落间的相似性关系应该是进行外来植物入侵预测的重要切入点,而功能性状的种间分化与种内变异可能是外来植物成功入侵的两种不同生态策略。在此基础上,该研究还通过物种功能性状的多维超体积构建了外来植物与乡土群落间的相似性,提出了基于这种相似性的外来植物入侵预测的研究框架和基本流程。该模型框架的建立有助于理解外来植物的入侵机制,对外来植物的潜在入侵性预测提供了理论依据。当然,要实现外来植物能否成功入侵的准确预测,不仅依赖于功能性状的选择,还要考虑入侵的生境依赖性、空间尺度的重要性以及乡土群落的可入侵性等,未来的研究重点是通过控制实验对该模型进行验证和进一步完善。     

Explanations for adaptations,just‐so stories,and limitations on evidence in evolutionary biology

Explanations of the historical origin of specific individual traits are a key part of the research program in paleontology and evolutionary biology. Why did bipedalism evolve in the human lineage? Why did some dinosaurs and related species have head crests? Why did viviparity evolve in some reptiles? Why did the common ancestor of primates evolve stereoscopic vision, grasping hands and feet, nails instead of claws, and large brains? These are difficult questions. To varying degrees, an explanation must grapple with (1) judgments about changes in fitness that might follow from a change in morphology – without actually observing behavior or measuring reproductive success, (2) the relationship between genes and traits, (3) limitations on doing relevant experiments, (4) the interpretation of causes that are almost certainly contingent, multifactorial, interactive, hierarchical, nonlinear, emergent, and probabilistic rather than deterministic, (5) limited information about variation and ontogeny, (6) a dataset based on the random fortunes of the historical record, including only partial hard‐tissue morphology and no soft‐tissue morphology, (7) an equally partial and problematic (for example, time‐averaged) record of the environment, (8) the compression of all data into a geological time scale that is likely to miss biologically important events or fluctuations, (9) dependence on a process that can only be inferred (“form and even behavior may leave fossil traces, but forces like natural selection do not”, ^1:130) and finally, (10) the assumption of the “adaptationist programme”² that the trait in question is in fact an adaptation rather than a consequence of genetic drift, correlated evolution, pleiotropy, exaptation, or other mechanisms.     

Studies on the effect of l-3,4-dehydroproline on collagen synthesis by chick embryo polysemes

Various proline analogs have been tested in vitro for their ability to inhibit the enzymatic aminoacylation of tRNA by proline. Of these, l-3,4-dehydroproline is the most potent inhibitor. This inhibition is competitive; the K_i is 100 μm. It was shown that l-3,4-dehydroproline can serve as substrate in the aminoacylation reaction. However, the incorporation of radioactivity from l-3,4-[¹⁴C]dehydroprolyl-tRNA into protein occurs at one-fifth the rate observed for l-prolyl-tRNA. The addition of l-3,4-dehydroproline in vitro inhibits the synthesis of collagen to a greater extent than non-collagen protein.     

Effect of APOE and a polygenic risk score on incident dementia and cognitive decline in a healthy older population

Few studies have measured the effect of genetic factors on dementia and cognitive decline in healthy older individuals followed prospectively. We studied cumulative incidence of dementia and cognitive decline, stratified by APOE genotypes and polygenic risk score (PRS) tertiles, in 12,978 participants of the ASPirin in Reducing Events in the Elderly (ASPREE) trial. At enrolment, participants had no history of diagnosed dementia, cardiovascular disease, physical disability or cognitive impairment. Dementia (adjudicated trial endpoint) and cognitive decline, defined as a >1.5 standard deviation decline in test score for either global cognition, episodic memory, language/executive function or psychomotor speed, versus baseline scores. Cumulative incidence for all‐cause dementia and cognitive decline was calculated with mortality as a competing event, stratified by APOE genotypes and tertiles of a PRS based on 23 common non‐APOE variants. During a median 4.5 years of follow‐up, 324 participants developed dementia, 503 died. Cumulative incidence of dementia to age 85 years was 7.4% in all participants, 12.6% in APOE ε3/ε4 and 26.6% in ε4/ε4. APOE ε4 heterozygosity/homozygosity was associated with a 2.5/6.3‐fold increased dementia risk and 1.4/1.8‐fold cognitive decline risk, versus ε3/ε3 (p < 0.001 for both). High PRS tertile was associated with a 1.4‐fold dementia risk versus low (CI 1.04–1.76, p = 0.02), but was not associated with cognitive decline (CI 0.96–1.22, p = 0.18). Incidence of dementia among healthy older individuals is low across all genotypes; however, APOE ε4 and high PRS increase relative risk. APOE ε4 is associated with cognitive decline, but PRS is not.     

Predicting the Risk of Suicide by Analyzing the Text of Clinical Notes

We developed linguistics-driven prediction models to estimate the risk of suicide. These models were generated from unstructured clinical notes taken from a national sample of U.S. Veterans Administration (VA) medical records. We created three matched cohorts: veterans who committed suicide, veterans who used mental health services and did not commit suicide, and veterans who did not use mental health services and did not commit suicide during the observation period (n = 70 in each group). From the clinical notes, we generated datasets of single keywords and multi-word phrases, and constructed prediction models using a machine-learning algorithm based on a genetic programming framework. The resulting inference accuracy was consistently 65% or more. Our data therefore suggests that computerized text analytics can be applied to unstructured medical records to estimate the risk of suicide. The resulting system could allow clinicians to potentially screen seemingly healthy patients at the primary care level, and to continuously evaluate the suicide risk among psychiatric patients.     

Caveolin-rich lipid rafts of the plasma membrane of mature cerebellar granule neurons are microcompartments for calcium/reactive oxygen and nitrogen species cross-talk signaling

In previous works, we have shown that L-type voltage-operated calcium channels, N-methyl-d-aspartate receptors (NMDAr), neuronal nitric oxide synthase (nNOS) and cytochrome b₅ reductase (Cb₅R) co-localize within the same lipid rafts-associated nanodomains in mature cerebellar granule neurons (CGN). In this work, we show that the calcium transport systems of the plasma membrane extruding calcium from the cytosol, plasma membrane calcium pumps (PMCA) and sodium–calcium exchangers (NCX), are also associated with these nanodomains. All these proteins were found to co-immunoprecipitate with caveolin-1 after treatment with 25 mM methyl-β-cyclodextrin, a lipid rafts solubilizing agent. However, the treatment of CGN with methyl-β-cyclodextrin largely attenuated the rise of cytosolic calcium induced by l-glutamate through NMDAr. Fluorescence energy transfer imaging revealed that all of them are present in sub-microdomains of a size smaller than 200 nm, with a peripheral distribution of the calcium extrusion systems PMCA and NCX. Fluorescence microscopy images analysis revealed high calcium dynamic sub-microcompartments near the plasma membrane in fura-2-loaded CGN at short times after addition of l-glutamate. In addition, the close proximity between sources of nitric oxide (nNOS) and superoxide anion (Cb₅R) suggests that these nanodomains are involved in the fast and efficient cross-talk between calcium and redox signaling in neurons.     

The modifying effects of fish oil on fasting ghrelin mRNA expression in weaned rats

Ghrelin expression and secretion seem to be influenced by the fat content of the diet. However, data on the probable adverse effect of high fat diet (HFD) with different dietary fats and saturation level of fatty acids is inconclusive. This study aimed at investigating the effects of HFDs on fasting total and acyl-ghrelin plasma levels, gastric fundus and duodenum ghrelin mRNA expressions. Weaned Wistar rats (n=50) were randomly divided to five groups of HFDs with fish oil (HF-F), olive oil (HF-O), soy oil (HF-S), butter (HF-B) and the controls. After 8weeks, blood samples were collected. While the animals were fasting for 24h, their blood and tissue samples were obtained. Plasma parameters of total and acyl ghrelin and ghrelin mRNA expression level in stomach and duodenum were measured. The HF-B fed group had lower fasting plasma acyl ghrelin level than the control, HF-F and HF-O groups (P<0.05); furthermore, the HF-F group had significantly higher acyl ghrelin level than the HF-S one (P<0.05). After feeding, all the groups, except for the HF-B one, had a significantly lower plasma acyl ghrelin levels (P<0.05), compared with the fasting state. Ghrelin mRNA expression levels in the gastric fundus and duodenum were significantly lower in the HF-B as compared to the control group. Furthermore, the HF-F group had significantly higher mRNA level in the duodenum, in comparison with the HF-B and HF-S groups. As HF-F and HF-O diets had the highest stimulatory effect on fasting ghrelin expression and plasma level, consumption of these dietary oils can play an important role in ghrelin regulation, which might affect feeding behavior and energy intake.     

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

Telomere length analysis of human mesenchymal stem cells by quantitative PCR

Human mesenchymal stem cells (hMSCs) have attracted much attention for tissue repair and wound healing because of their self-renewal capacity and multipotentiality. In order to mediate an effective therapy, substantial numbers of cells are required, which necessitates extensive sub-culturing and expansion of hMSCs. Throughout ex vivo expansion, the cells undergo telomere shortening, and critically short telomeres can trigger loss of cell viability. Telomeres are nucleoprotein structures that cap the ends of chromosomes, and serve to protect the DNA from the degradation which occurs due to the end-replication problem in all eukaryotes. As hMSCs have only a finite ability for self-renewal like most somatic cells, assaying for telomere length in hMSCs provides critical information on the replicative capacity of the cells, an important criterion in the selection of hMSCs for therapy. Telomere length is generally quantified by Southern blotting and fluorescence in situ hybridization, and more recently by PCR-based methods. Here we describe the quantification of hMSC telomere length by real-time PCR; our results demonstrate the effect of telomere shortening on the proliferation and clonogenicity of hMSCs. Thus, this assay constitutes a useful tool for the determination of relative telomere length in hMSCs.     

Hydrodynamic behaviors in fermentative hydrogen bioreactors by pressure fluctuation analysis

Three bioreactor configurations were employed in these investigations, which consisted of working volumes of 10, 1.2 and 1.2 L. Power spectrum diagrams of bed pressure fluctuation were used with hydraulic retention times (HRT) and geometric factors to identify the flow regimes in the bioreactors, where HRT varied from 8 to 1 h. It was found that the flow regimes in the bioreactors changed from a dispersed regime to coalesced and slugging regimes, when the biogas production rate (BPR) increased, as a result of decreasing the operating HRT. The flow regime was a dispersed bubble regime when the HRT was higher than 4 h in the bioreactor, whereas when the HRT was 2 h the coalesced bubble phenomena occurred in the bioreactor. A slugging regime was found when the HRT was lower than 1 h in thinner bioreactor.