Current capacity,bottlenecks, and future projections for offsetting habitat loss using Mitigation and Conservation banking in the United States

Habitat banking in its many iterations is an established and popular mechanism to deliver environmental offsets. The United States can look back at over 30 years of banking experience with the underlying framework and policies being consistently updated and improved. Given the increased demand in habitat banking, we provide insights into how bank area capacity is distributed across the United States for four different bank targets (wetlands, streams, multiple ecosystems, species) based on information extracted from the Regulatory In-lieu Fee and Bank Information Tracking System, as well as, estimating future capacities and area reserves through a predictive modeling approach based on data from the past 26 years. Future predictions indicate a decrease in available reserves for banks targeting wetlands or multiple ecosystems, with potential bottlenecks relating to large reserves being limited to the southeast and release schedules not catching up to the current and anticipated demand. Banks targeting species or streams are predicted to meet future demand, with species banks (conservation banks) following a different legislative and operational approach based on the listing of endangered species and pro-active approaches with anticipated future demand. Most current reserves for all four bank types are restricted to very few service areas with around one-third of all bank areas still awaiting release, limiting their availability on a broader scale. Strategic planning networks are necessary to meet future demand on a national scale and to identify areas suitable for banking or likely to experience future environmental or developmental stress.     

Automatic determination of the handedness of single-particle maps of macromolecules solved by CryoEM

Single-Particle Analysis by Cryo-Electron Microscopy is a well-established technique to elucidate the three-dimensional (3D) structure of biological macromolecules. The orientation of the acquired projection images must be initially estimated without any reference to the final structure. In this step, algorithms may find a mirrored version of all the orientations resulting in a mirrored 3D map. It is as compatible with the acquired images as its unmirrored version from the image processing point of view, only that it is not biologically plausible.In this article, we introduce HaPi (Handedness Pipeline), the first method to automatically determine the hand of electron density maps of macromolecules solved by CryoEM. HaPi is built by training two 3D convolutional neural networks. The first determines α-helices in a map, and the second determines whether the α-helix is left-handed or right-handed. A consensus strategy defines the overall map hand. The pipeline is trained on simulated and experimental data. The handedness can be detected only for maps whose resolution is better than 5 Å. HaPi can identify the hand in 89% of new simulated maps correctly. Moreover, we evaluated all the maps deposited at the Electron Microscopy Data Bank and 11 structures uploaded with the incorrect hand were identified.     

Expression and functional analysis of flotillins in Dugesia japonica

FLOTILLIN-1 and FLOTILLIN-2 are membrane rafts associated proteins that have been implicated in insulin and growth factor signaling, endocytosis, cell migration, proliferation, differentiation, cytoskeleton remodeling and membrane trafficking. Furthermore, FLOTILLINs also play important roles in the progression of cancer and neurodegenerative diseases. In this study, the roles of flotillins are investigated in planarian Dugesia japonica. The results show that Djflotillin-1 and Djflotillin-2 play a key role in homeostasis maintenance and regeneration process by regulating the proliferation of the neoblast cells, they are not involved in the maintenance and regeneration of the central nervous system in planarians.     

Development of a novel MATLAB-based framework for implementing mechanical joint stability constraints within OpenSim musculoskeletal models

The Static Optimization (SO) solver in OpenSim estimates muscle activations and forces that only equilibrate applied moments. In this study, SO was enhanced through an open-access MATLAB interface, where calculated muscle activations can additionally satisfy crucial mechanical stability requirements. This Stability-Constrained SO (SCSO) is applicable to many OpenSim models and can potentially produce more biofidelic results than SO alone, especially when antagonistic muscle co-contraction is required to stabilize body joints. This hypothesis was tested using existing models and experimental data in the literature. Muscle activations were calculated by SO and SCSO for a spine model during two series of static trials (i.e. simulation 1 and 2), and also for a lower limb model (supplementary material 2). In simulation 1, symmetric and asymmetric flexion postures were compared, while in simulation 2, various external load heights were compared, where increases in load height did not change the external lumbar flexion moment, but necessitated higher EMG activations. During the tasks in simulation 1, the predicted muscle activations by SCSO demonstrated less average deviation from the EMG data (6.8% −7.5%) compared to those from SO (10.2%). In simulation 2, SO predicts constant muscle activations and forces, while SCSO predicts increases in the average activations of back and abdominal muscles that better match experimental data. Although the SCSO results are sensitive to some parameters (e.g. musculotendon stiffness), when considering the strategy of the central nervous system in distributing muscle forces and in activating antagonistic muscles, the assigned activations by SCSO are more biofidelic than SO.     

Alterations to plasma membrane lipid contents affect the biophysical properties of erythrocytes from individuals with hypertension

Genetic and environmental factors may contribute to high blood pressure, which is termed essential hypertension. Hypertension is a major independent risk factor for cardiovascular disease, stroke and renal failure; thus, elucidation of the etiopathology of hypertension merits further research. We recently reported that the platelets and neutrophils of patients with hypertension exhibit altered biophysical characteristics. In the present study, we assessed whether the major structural elements of erythrocyte plasma membranes are altered in individuals with hypertension. We compared the phospholipid (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, sphingosine) and cholesterol contents of erythrocytes from individuals with hypertension (HTN) and healthy individuals (HI) using LC/MS-MS. HTN erythrocytes contained higher phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine contents and a lower cholesterol content than HI erythrocytes. Furthermore, atomic force microscopy revealed important morphological changes in HTN erythrocytes, which reflected the increased membrane fragility and fluidity and higher levels of oxidative stress observed in HTN erythrocytes using spectrophotofluorometry, flow cytometry and spectrometry. This study reveals that alterations to the lipid contents of erythrocyte plasma membranes occur in hypertension, and these alterations in lipid composition result in morphological and physiological abnormalities that modify the dynamic properties of erythrocytes and contribute to the pathophysiology of hypertension.     

三峡库区水体中固氮微生物多样性及其影响因素

【目的】研究分析不同时空条件下三峡库区水体固氮微生物多样性,并探讨其与地球化学参数的相关性。【方法】采集三峡库区不同时间(三月份和六月份)和空间(干流与支流)的水体样品,对其进行地球化学参数分析,并通过构建克隆文库分析样品中固氮功能基因(nifH)的多样性进而探讨其与水体地化参数的相关关系。【结果】统计分析显示三峡库区水体固氮微生物α-多样性和群落组成具有时空差异。支流水体样品的固氮微生物α-多样性高于干流水体样品;六月水体样品的固氮微生物α-多样性高于三月水体样品。三峡库区三月水体样品中的固氮微生物群落以Proteobacteria (50.3%)和Firmicutes (40.0%)为主;六月水体样品的固氮微生物群落以Proteobacteria(48.4%)、Firmicutes(25.4%)和Cyanobacteria(19.0%)为主。Mantel检验结果显示:固氮微生物群落结构的差异与温度、pH和DIC等地球化学参数具有显著(P0.05)相关性,其中温度和pH的相关性系数最大。【结论】三峡库区固氮微生物的种群结构和多样性具有时空差异,影响三峡水库水体中固氮微生物群落结构与多样性的主要环境因素为温度和pH,同时浊度、DIC、氨氮也对库区水体固氮微生物群落结构和多样性有一定的影响。     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

Population trends for humpback whales (Megaptera novaeangliae) foraging in the Francisco Coloane Coastal‐Marine Protected Area,Magellan Strait,Chile

In 2003 a feeding aggregation of southeastern Pacific humpback whales (Megaptera novaeangliae) was reported in the Magellan Strait. While Chile established its first marine national park in the Strait to protect humpback whale habitat, fatal ship strikes remain a concern because of overlap with a busy shipping lane. To better understand population risk, we estimated abundance and survival for this population using Bayesian robust‐design mark‐recapture models fit to photographic data from 2004 to 2016. Overall, the model estimated a total of 204 whales (95% CI: 199–210) during the last 12 yr, and 93 (95% CI: 86–100) in the 2016/2017 austral summer. The population grew at 2.3% (CI: 2.1%–3.1%), an annual increase of two whales. Annual survival (including calves) was estimated at 0.892 (CI: 0.871–0.910). Our results corroborate a persistent feeding population, but one that is increasing relatively slowly. Owing to its vulnerability stemming from its small size, coupled with significant overlap with a busy shipping lane, we argue this subpopulation is at significant risk from ship strikes and may be one of the few populations where anthropogenic mortalities could regulate population dynamics. We therefore encourage continued monitoring via photographic mark‐resighting surveys, and analyses explicitly investigating potential population‐level ship strike effects.     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。