Targeted disruption of mouse Coch provides functional evidence that DFNA9 hearing loss is not a COCH haploinsufficiency disorder

Dominant progressive hearing loss and vestibular dysfunction DFNA9 is caused by mutations of the human COCH gene. COCH encodes cochlin, a highly abundant secreted protein of unknown function in the inner ear. Cochlin has an N-terminal LCCL domain followed by two vWA domains, and all known DFNA9 mutations are either missense substitutions or an amino acid deletion in the LCCL domain. Here, we have characterized the auditory phenotype associated with a genomic deletion of mouse Coch downstream of the LCCL domain. Homozygous Coch ^−/− mice express no detectable cochlin in the inner ear. Auditory brainstem responses to click and pure-tone stimuli (8, 16, 32 kHz) were indistinguishable among wild type and homozygous Coch ^−/− mice. A Coch-LacZΔneo reporter allele detected Coch mRNA expression in nonsensory epithelial and stromal regions of the cochlea and vestibular labyrinth. These data provide functional evidence that DFNA9 is probably not caused by COCH haploinsufficiency, but via a dominant negative or gain-of-function effect, in nonsensory regions of the inner ear.Tomoko Makishima, Clara I. Rodriguez contributed equally     

优于单一最大熵生态位模型的混合烟粉虱生境风险评估模型

预测入侵生物的潜在地理分布、快速评估其高脆弱性区域是实现入侵生物前瞻性风险预警的重要手段。MaxEnt生态位模型是目前应用最广泛的生境风险评估方法,操作简单,预测精度较高,但模型对数据的质量和数量过分依赖。以烟粉虱Bemisia tabaci为对象,引入地理探测器显式描述评价因子的空间关联规律和贡献度,结合MaxEnt生态位模型,提出一种混合生境风险评估模型(Geo-MaxEnt),并与单一MaxEnt生态位模型进行对比。结果表明：(1)地理探测器模型显示,海拔(0.56)、土地利用(0.43)、最热月最高温度(0.36)和年平均温度(0.30),对烟粉虱的空间分布具有显著影响,各因子对烟粉虱生境的影响存在显著的差异。海拔和土地利用PD值最高,是影响烟粉虱生境的主要驱动因子。环境因子的交互作用强化了各个因子的影响力。(2)单一MaxEnt生态位和所构建的模型总体精度分别是94.86%(AUC 0.91)和98.13%(AUC 0.94),相较之下,所构建的模型精度略高,表明所构建的模型是合理的,具有高度的可靠性;(3)对于高风险区,混合模型优于MaxEnt模型,但两者在空间分布方面高度...     

Targeted therapy for the loss of von Hippel-Lindau in renal cell carcinoma: a novel molecule that induces autophagic cell death

Radiation and conventional cytotoxic chemotherapies are ineffective in treating renal cancer. Approximately 75 percent of renal cell carcinoma (RCC) is associated with an inactivation of the tumor suppressor gene von Hippel-Lindau (VHL). We exploited the possibility of targeting VHL-deficient RCC through synthetic lethality using a high-throughput screening approach. In this screen, STF-62247 was identified to be selectively toxic and growth inhibitory to renal cells lacking VHL. We recently demonstrated that the cytotoxicity of STF-62247 is due to dysregulated autophagy. Furthermore, the reduction of protein levels of essential autophagy pathway components such as Atg5, Atg7 and Atg9 reduces sensitivity of VHL-deficient cells to killing by STF-62247. Loss of proteins involved in Golgi trafficking sensitized RCC with wild-type VHL to killing by STF-62247, indicating a potential role for these proteins as a target of the compound. Our study supports the concept of using synthetic lethality to selectively kill VHL-deficient cells that represents a new type of targeted therapy for the treatment of RCC.     

A CORF computational model of a simple cell that relies on LGN input outperforms the Gabor function model

Simple cells in primary visual cortex are believed to extract local contour information from a visual scene. The 2D Gabor function (GF) model has gained particular popularity as a computational model of a simple cell. However, it short-cuts the LGN, it cannot reproduce a number of properties of real simple cells, and its effectiveness in contour detection tasks has never been compared with the effectiveness of alternative models. We propose a computational model that uses as afferent inputs the responses of model LGN cells with center–surround receptive fields (RFs) and we refer to it as a Combination of Receptive Fields (CORF) model. We use shifted gratings as test stimuli and simulated reverse correlation to explore the nature of the proposed model. We study its behavior regarding the effect of contrast on its response and orientation bandwidth as well as the effect of an orthogonal mask on the response to an optimally oriented stimulus. We also evaluate and compare the performances of the CORF and GF models regarding contour detection, using two public data sets of images of natural scenes with associated contour ground truths. The RF map of the proposed CORF model, determined with simulated reverse correlation, can be divided in elongated excitatory and inhibitory regions typical of simple cells. The modulated response to shifted gratings that this model shows is also characteristic of a simple cell. Furthermore, the CORF model exhibits cross orientation suppression, contrast invariant orientation tuning and response saturation. These properties are observed in real simple cells, but are not possessed by the GF model. The proposed CORF model outperforms the GF model in contour detection with high statistical confidence (RuG data set: p < 10⁻⁴, and Berkeley data set: p < 10⁻⁴). The proposed CORF model is more realistic than the GF model and is more effective in contour detection, which is assumed to be the primary biological role of simple cells.     

Targeted therapy for the loss of von Hippel-Lindau in renal cell carcinoma: A novel molecule that induces autophagic cell death

Radiation and conventional cytotoxic chemotherapies are ineffective in treating renal cancer. Approximately 75% of renal cell carcinoma (RCC) is associated with an inactivation of the tumor suppressor gene von Hippel-Lindau (VHL). We exploited the possibility of targeting VHL-deficient RCC through synthetic lethality using a high-throughput screening approach. In this screen, STF-62247 was identified to be selectively toxic and growth inhibitory to renal cells lacking VHL. We recently demonstrated that the cytotoxicity of STF-62247 is due to dysregulated autophagy. Furthermore, the reduction of protein levels of essential autophagy pathway components such as Atg5, Atg7 and Atg9 reduces sensitivity of VHL-deficient cells to killing by STF-62247. Loss of proteins involved in Golgi trafficking sensitized RCC with wild-type VHL to killing by STF-62247, indicating a potential role for these proteins as a target of the compound. Our study supports the concept of using synthetic lethality to selectively kill VHL-deficient cells that represents a new type of targeted therapy for the treatment of RCC.

Addendum to: Turcotte S, Chan DA, Sutphin PD, Hay MP, Denny WA, Giaccia AJ. A molecule targeting VHL-deficient renal cell carcinoma that induces autophagy. Cancer Cell 2008; 14:90-102.     

Meta‐analysis shows that environmental DNA outperforms traditional surveys,but warrants better reporting standards

1. Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost‐effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta‐analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently “better.”
2. Environmental DNA publications for multiple species or single macro‐organism detection were identified using the Web of Science, by searching “eDNA” and “environmental DNA” across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.
3. Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa‐dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance.
4. Synthesis and applications: The results of this meta‐analysis demonstrate that where there is a direct comparison, eDNA surveys of macro‐organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods‐based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

     

Effect of salcatonin given intranasally on early postmenopausal bone loss.

OBJECTIVE--To study the effect of salmon calcitonin (salcatonin) given intranasally on calcium and bone metabolism in early postmenopausal women. DESIGN--Double blind, placebo controlled, randomised group comparison. SETTING--Outpatient clinic for research into osteoporosis. SUBJECTS--52 Healthy women who had had a natural menopause two and a half to five years previously. INTERVENTIONS--The 52 women were allocated randomly to two years of treatment with either salcatonin 100IU given intranasally (n = 26) or placebo (n = 26). Both groups received a calcium supplement of 500 mg daily. Seven of the women receiving salcatonin and six of those receiving placebo left the study before its end. MAIN OUTCOME MEASURES--Bone mineral content in the spine, the total skeleton, and the forearms after two years of treatment. RESULTS--Bone mineral content in the spine was significantly higher in the women who had received salcatonin than in those who had received placebo both after one year and after two years of treatment. After one year the difference was 3.8% (95% confidence interval 0.0 to 7.6%) and after two years it was 8.2% (3.8 to 12.6%). In contrast, the bone mineral content in the distal and proximal forearms and in the total skeleton declined similarly in both groups by about 2% each year, and after two years of treatment the differences between the groups were not significant. Biochemical estimates of bone turnover were not affected by salcatonin. CONCLUSION--The results suggest that salcatonin given intranasally in the dose used prevents bone loss in the spine of early post menopausal women but does not affect the peripheral skeleton.     

Comparative evaluation of a new effective population size estimator based on approximate bayesian computation

We describe and evaluate a new estimator of the effective population size (N(e)), a critical parameter in evolutionary and conservation biology. This new "SummStat" N(e) estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N(e). Simulations of a Wright-Fisher population with known N(e) show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N(e) values. We also address the paucity of information about the relative performance of N(e) estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and N(e) < or = 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N(e). The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data.     

An estimator of the Opportunity for Selection that is independent of mean fitness

Variation among individuals in number of offspring (fitness, k) sets an upper limit to the evolutionary response to selection. This constraint is quantified by Crow's Opportunity for Selection (I), which is the variance in relative fitness (I = σ²_k/(u_k)²). Crow's I has been widely used but remains controversial because it depends on mean offspring number in a sample (). Here, I used a generalized Wright-Fisher model that allows for unequal probabilities of producing offspring to evaluate behavior of Crow's I and related indices under a wide range of sampling scenarios. Analytical and numerical results are congruent and show that rescaling the sample variance (s²_k) to its expected value at a fixed removes dependence of I on mean offspring number, but the result still depends on choice of . A new index is introduced, Δ_I = Π– E(Î_drift) = Π– 1/, which makes Î independent of sample without the need for variance rescaling. Δ_I has a straightforward interpretation as the component of variance in relative fitness that exceeds that expected under a null model of random reproductive success. Δ_I can be used to directly compare estimates of the Opportunity for Selection for samples from different studies, different sexes, and different life stages.     

Targeted deletion of the tub mouse obesity gene reveals that tubby is a loss-of-function mutation

The mouse tubby phenotype is characterized by maturity-onset obesity accompanied by retinal and cochlear degeneration. A positional cloning effort to find the gene responsible for this phenotype led to the identification of tub, a member of a novel gene family of unknown function. A splice defect mutation in the 3' end of the tub gene, predicted to disrupt the C terminus of the Tub protein, has been implicated in the genesis of the tubby phenotype. It is not clear, however, whether the Tub mutant protein retains any biological activity, or perhaps has some dominant function, nor is it established that the tubby mutation is itself responsible for all of the observed tubby phenotypes. To address these questions, we generated tub-deficient mice and compared their phenotype to that of tubby mice. Our results demonstrate that tubby is a loss-of-function mutation of the tub gene and that loss of the tub gene is sufficient to give rise to the full spectrum of tubby phenotypes. We also demonstrate that loss of photoreceptors in the retina of tubby and tub-deficient mice occurs by apoptosis. In addition, we show that Tub protein expression is not significantly altered in the ob, db, or melanocortin 4 receptor-deficient mouse model of obesity.     

Estimation of river ecosystem biodiversity based on the Chao estimator

The research was focused on identification of plant diversity assessment approach which would be suitable for flowing waters. Moreover, the study attempted to estimate the extent of the survey (sampling effort) needed for detection of full plant diversity in river ecosystems. The analysed data were collected in a botanical survey carried out on the lowland sandy bottom Wel river, which is a very common river type in Europe. The Chao method of estimation of total species richness of macrophytes and Hill numbers were used to estimate the diversity based on very common plants (inverse Simpson index) as well as frequent species (Shannon index) and also including rare species (species richness). The analysis showed that using standard macrophyte survey approach for rivers, it is relatively easy to record abundant plants, but it is not possible to detect all species, because many aquatic macrophytes occur with low frequency and abundance requiring enormous sampling effort to detect all of them. It exceeds capabilities of most scientific projects. To improve the accuracy of diversity estimation, the rarefaction and extrapolation method was recommended. This method can reduce the bias in diversity estimates based on limited observational data, and thus limit inaccurate conclusions and subsequent wrong decisions in the conservation frameworks related to freshwater protection.     

A protein folding potential that places the native states of a large number of proteins near a local minimum

Background

We present a simple method to train a potential function for the protein folding problem which, even though trained using a small number of proteins, is able to place a significantly large number of native conformations near a local minimum. The training relies on generating decoys by energy minimization of the native conformations using the current potential and using a physically meaningful objective function (derivative of energy with respect to torsion angles at the native conformation) during the quadratic programming to place the native conformation near a local minimum.

Results

We also compare the performance of three different types of energy functions and find that while the pairwise energy function is trainable, a solvation energy function by itself is untrainable if decoys are generated by minimizing the current potential starting at the native conformation. The best results are obtained when a pairwise interaction energy function is used with solvation energy function.

Conclusions

We are able to train a potential function using six proteins which places a total of 42 native conformations within ~4 Å rmsd and 71 native conformations within ~6 Å rmsd of a local minimum out of a total of 91 proteins. Furthermore, the threading test using the same 91 proteins ranks 89 native conformations to be first and the other two as second.     

海洋最小含氧带氮流失过程与机制

对全球大洋氮循环的研究发现,大洋输入和输出的氮存在严重的不平衡,所固定的氮中有相当一部分被还原为N₂或N₂O从大洋中流失,而海洋最小含氧带(OMZ)被认为是发生氮流失的最主要区域,通过反硝化作用和厌氧氨氧化作用,固定氮在OMZ海区内损失量可达40～450 Tg·a^-1.对不同海区OMZ内固定氮损失的两种主要作用总结发现,异养反硝化作用在热带太平洋东部、阿拉伯海的OMZ内以及海洋沉积物内占有显著优势,在智利、秘鲁沿岸海域及阿拉伯海域也已发现自养反硝化作用的存在;而在黑海、非洲西南部的本格拉上升流、智利北部沿岸等地,厌氧氨氧化作用强烈,且其在陆架区的作用强度和面积要大于大洋区.OMZ氮的流失除受氮流失过程自身影响外,固氮作用、硝化作用、硝酸盐异化还原作用等都可能对OMZ海区内氮收支不平衡造成影响.其中固氮作用的影响最不能忽视,其在全球OMZ内固定的氮的总量可达15～40 Tg·a^-1,是对OMZ氮流失量的重要补充.区分反硝化作用和厌氧氨氧化作用对OMZ氮流失的相对贡献,明确氮流失的另一产物N₂O的形成机制和定量评估方法是当前OMZ氮流失研究中存在的最主要问题.本文针对存在问题提出了相应的研究设想,以期为海洋最小含氧带的研究提供参考.     

Targeted depletion of hepatic ACAT2-driven cholesterol esterification reveals a non-biliary route for fecal neutral sterol loss

Deletion of acyl-CoA:cholesterol O-acyltransferase 2 (ACAT2) in mice results in resistance to diet-induced hypercholesterolemia and protection against atherosclerosis. Recently, our group has shown that liver-specific inhibition of ACAT2 via antisense oligonucleotide (ASO)-mediated targeting likewise limits atherosclerosis. However, whether this atheroprotective effect was mediated by: 1) prevention of packaging of cholesterol into apoB-containing lipoproteins, 2) augmentation of nascent HDL cholesterol secretion, or 3) increased hepatobiliary sterol secretion was not examined. Therefore, the purpose of these studies was to determine whether hepatic ACAT2 is rate-limiting in all three of these important routes of cholesterol homeostasis. Liver-specific depletion of ACAT2 resulted in reduced packaging of cholesterol into apoB-containing lipoproteins (very low density lipoprotein, intermediate density lipoprotein, and low density lipoprotein), whereas high density lipoprotein cholesterol levels remained unchanged. In the liver of ACAT2 ASO-treated mice, cholesterol ester accumulation was dramatically reduced, yet there was no reciprocal accumulation of unesterified cholesterol. Paradoxically, ASO-mediated depletion of hepatic ACAT2 promoted fecal neutral sterol excretion without altering biliary sterol secretion. Interestingly, during isolated liver perfusion, ACAT2 ASO-treated livers had augmented secretion rates of unesterified cholesterol and phospholipid. Furthermore, we demonstrate that liver-derived cholesterol from ACAT2 ASO-treated mice is preferentially delivered to the proximal small intestine as a precursor to fecal excretion. Collectively, these studies provide the first insight into the hepatic itinerary of cholesterol when cholesterol esterification is inhibited only in the liver, and provide evidence for a novel non-biliary route of fecal sterol loss.