Demographic responses to climate‐driven variation in habitat quality across the annual cycle of a migratory bird species

The demography and dynamics of migratory bird populations depend on patterns of movement and habitat quality across the annual cycle. We leveraged archival GPS‐tagging data, climate data, remote‐sensed vegetation data, and bird‐banding data to better understand the dynamics of black‐headed grosbeak (Pheucticus melanocephalus) populations in two breeding regions, the coast and Central Valley of California (Coastal California) and the Sierra Nevada mountain range (Sierra Nevada), over 28 years (1992–2019). Drought conditions across the annual cycle and rainfall timing on the molting grounds influenced seasonal habitat characteristics, including vegetation greenness and phenology (maturity dates). We developed a novel integrated population model with population state informed by adult capture data, recruitment rates informed by age‐specific capture data and climate covariates, and survival rates informed by adult capture–mark–recapture data and climate covariates. Population size was relatively variable among years for Coastal California, where numbers of recruits and survivors were positively correlated, and years of population increase were largely driven by recruitment. In the Sierra Nevada, population size was more consistent and showed stronger evidence of population regulation (numbers of recruits and survivors negatively correlated). Neither region showed evidence of long‐term population trend. We found only weak support for most climate–demographic rate relationships. However, recruitment rates for the Coastal California region were higher when rainfall was relatively early on the molting grounds and when wintering grounds were relatively cool and wet. We suggest that our approach of integrating movement, climate, and demographic data within a novel modeling framework can provide a useful method for better understanding the dynamics of broadly distributed migratory species.     

An application of the theoretical group methods to modeling of complex systems

The applicability of theoretical group methods to studying complex physical and biological systems with the potential of self-organization was demonstrated. The problem of calculating climate sensitivity parameters taking into account the cyclone-anticyclone structure of the atmosphere optically dense in the infrared region is considered as an example.     

Acetic acid and acidification accelerate chronological and replicative aging in yeast

Comment on: Murakami C, et al. Cell Cycle 2012; 11:3087-96.     

Technologies for integrating biological data

The process of building a new database relevant to some field of study in biomedicine involves transforming, integrating and cleansing multiple data sources, as well as adding new material and annotations. This paper reviews some of the requirements of a general solution to this data integration problem. Several representative technologies and approaches to data integration in biomedicine are surveyed. Then some interesting features that separate the more general data integration technologies from the more specialised ones are highlighted.     

Synchrony of Seed Dispersal, Hydrology and Local Climate in a Semi-arid River Reach in California

The temporal availability of propagules is a critical factor in sustaining pioneer riparian tree populations along snowmelt-driven rivers because seedling establishment is strongly linked to seasonal hydrology. River regulation in semi-arid regions threatens to decouple seed development and dispersal from the discharge regime to which they evolved. Using the lower Tuolumne River as a model system, we quantified and modeled propagule availability for Populus fremontii (POFR), Salix gooddingii (SAGO), and Salix exigua (SAEX), the tree and shrub species that dominate near-channel riparian stands in the San Joaquin Basin, CA. A degree-day model was fit to field data of seasonal seed density and local temperature from three sites in 2002–2004 to predict the onset of the peak dispersal period. To evaluate historical synchrony of seed dispersal and seasonal river hydrology, we compared peak spring runoff timing to modeled peak seed release periods for the last 75 years. The peak seed release period began on May 15 for POFR (range April 23–June 10), May 30 for SAGO (range May 19–June 11) and May 31 for SAEX (range May 8–June 30). Degree-day models for the onset of seed release reduced prediction error by 40–67% over day-of-year means; the models predicted best the interannual, versus site-to-site, variation in timing. The historical analysis suggests that POFR seed release coincided with peak runoff in almost all years, whereas SAGO and SAEX dispersal occurred during the spring flood recession. The degree-day modeling approach reduce uncertainty in dispersal timing and shows potential for guiding flow releases on regulated rivers to increase riparian tree recruitment at the lowest water cost.     

Plant physiology in theory and practice: An analysis of the WBE model for vascular plants

The theoretical model of West, Brown and Enquist (hereafter WBE) proposed the fractal geometry of the transport system as the origin of the allometric scaling laws observed in nature. The WBE model has either been criticized for some restrictive and biologically unrealistic constraints or its reliability debated on the evidence of empirical tests. In this work, we revised the structure of the WBE model for vascular plants, highlighting some critical assumptions and simplifications and discuss them with regard to empirical evidence from plant anatomy and physiology. We conclude that the WBE model had the distinct merit of shedding light on some important features such as conduit tapering. Nonetheless, it is over-simplistic and a revised model would be desirable with an ontogenetic perspective that takes some important phenomena into account, such as the transformation of the inner sapwood into heartwood and the effect of hydraulic constraints in limiting the growth in height.     

Poplar genomics is getting popular: the impact of the poplar genome project on tree research

Trees, due to their long life-span, have characteristics that distinguish them from annual, herbaceous plants. It is likely that many of these properties are based on a tree-specific genetic foundation. The U.S. Department of Energy initiated a genome-sequencing project for Populus, a model perennial plant. Through international collaboration and input to the sequencing effort, the annotated whole genome sequence of Populus trichocarpa will be released to the public in early 2004. This genomic resource will, for the first time, allow comparison between a perennial and an annual plant on a whole genome basis and therefore provide clues for molecular research on tree-specific questions like dormancy, development of a secondary cambium, juvenile-mature phase change, or long-term host-pest interactions. The approximately 520 Mbp of annotated genomic sequence will complement and expand the knowledge provided so far by the 125,000 ESTs from poplar that are available in public databases. This article introduces the international poplar research programmes and points out the significance of the poplar genome project for plant research.     

原发性肝癌患者术后癌因性疲乏的影响因素及其预测模型构建

摘要 目的：分析原发性肝癌患者术后癌因性疲乏（CRF）的影响因素并构建预测模型。方法：选取2020年1月～2023年1月湖南师范大学附属第一医院收治接受手术治疗的200例原发性肝癌患者,根据术后3个月是否存在CRF将患者分为CRF组（124例）和非CRF组（76例）。单因素和多因素Logistic回归分析影响原发性肝癌患者术后CRF的因素并构建其预测模型。通过受试者工作特征（ROC）曲线分析预测模型对原发性肝癌患者术后CRF的预测价值。结果：单因素分析显示,CRF组病程长于非CRF组,Child-Pugh分级B级、美国东部肿瘤协作组功能状态（ECOG）评分1～2分、辅助化疗、医疗付费方式自费、抑郁/焦虑比例高于非CRF组,文化程度高中及以上、家庭月收入＞3000元、高度社会支持度比例低于非CRF组（P＜0.05）。多因素Logistic回归分析显示,病程延长、Child-Pugh分级B级、ECOG评分1～2分、辅助化疗、医疗付费方式自费、抑郁/焦虑为影响原发性肝癌患者术后CRF的独立危险因素,家庭月收入＞3000元、高度社会支持为独立保护因素（P＜0.05）。原发性肝癌患者术后CRF的预测模型方程：Logit（P）=P/1-P=-1.252+0.409×病程+0.839×Child-Pugh分级+1.378×ECOG评分+1.055×辅助化疗+1.476×医疗付费方式-0.793×家庭月收入+0.883×抑郁/焦虑-1.260×社会支持度。霍斯默-莱梅肖检验P＞0.05。ROC曲线分析显示,模型预测原发性肝癌患者术后CRF的曲线下面积为0.910,敏感度为87.10%,特异度为85.53%。结论：病程、Child-Pugh分级、ECOG评分、辅助化疗、医疗付费方式、抑郁/焦虑、家庭月收入、社会支持度为影响原发性肝癌患者术后CRF的因素,基于此构建的预测模型对原发性肝癌患者术后CRF的预测价值较高,可能有助于临床早期发现和干预原发性肝癌患者术后CRF,以改善患者预后。     

Thermal effects in stretching of Go-like models of titin and secondary structures

The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases, thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly at low temperatures. However, differences in bonding geometry lead to different sensitivity to temperature and different changes in the unfolding pattern. Due to its special native-state geometry, titin is much more thermally and elastically stable than the secondary structures. At low temperatures, serial repeats of titin show a parallel unfolding of all domains to an intermediate state, followed by serial unfolding of the domains. At high temperatures, all domains unfold simultaneously, and the unfolding distance decreases monotonically with the contact order, that is, the sequence distance between the amino acids that form the native contact.     

Mechanistic insights into the inhibition of prostate specific antigen by beta-lactam class compounds

Prostate Specific Antigen (PSA) is a biomarker used in the diagnosis of prostate cancer and to monitor therapeutic response. However, its precise role in prostate carcinogenesis and metastasis remains largely unknown. A number of studies arguing in the favor of an active role of PSA in prostate cancer development and progression have implicated this serine protease in the release and activation of growth factors such as insulin-like growth factor 1 (IGF1) through cleavage of insulin like growth factor binding protein 3 and Transforming Growth Factor beta (TGF-beta) through cleavage of Latent TGF-beta. In contrast, other studies suggest that PSA activity might hinder tumor development and progression. In light of these contradictory findings, efficient inhibitors of PSA are needed for exploring its biological role in tumor development and metastasis. Towards the goal of developing potent inhibitors of PSA, we have explored the molecular mechanism of a series of beta-lactam based compounds on binding to PSA using activity assays, matrix assisted laser desorption ionization with a time-of-flight mass spectrometry, and GOLD docking methodology. The mass spectrometry experiments and the activity assays confirmed the time-dependent and covalent nature of beta-lactam binding. To gain insights on the reaction intermediates at the molecular level, we docked beta-lactam inhibitors to a homology modeled PSA using the GOLD docking program in noncovalent and covalent binding modes. The docking studies elucidated the molecular details of the early noncovalent Michaelis complex, the acyl-enzyme covalent complex, and the nature of conformational reorganization required for the long term stability of the covalent complex. Additionally, the molecular basis for the effect of stereochemistry of the lactam ring on the inhibitory potency was elucidated through docking of beta-lactam enantiomers. As a validation of our docking methodology, two novel enantiomers were synthesized and evaluated for their inhibitory potency using fluorogenic substrate based activity assays. Additionally, cis enantiomers of eight beta-lactam compounds reported in a previous study were docked and their GOLD scores and binding modes were analyzed in order to assess the general applicability of our docking results. The close agreement of our docking results with the experimental data validates the mechanistic insights revealed through the docking studies and paves the way for the design and development of potent and specific inhibitors of PSA.