Parameter estimation for discretely observed linear birth‐and‐death processes

Birth‐and‐death processes are widely used to model the development of biological populations. Although they are relatively simple models, their parameters can be challenging to estimate, as the likelihood can become numerically unstable when data arise from the most common sampling schemes, such as annual population censuses. A further difficulty arises when the discrete observations are not equi‐spaced, for example, when census data are unavailable for some years. We present two approaches to estimating the birth, death, and growth rates of a discretely observed linear birth‐and‐death process: via an embedded Galton‐Watson process and by maximizing a saddlepoint approximation to the likelihood. We study asymptotic properties of the estimators, compare them on numerical examples, and apply the methodology to data on monitored populations.     

华生关怀理论对老年痴呆症患者的临床干预效果

目的:探索华生关怀理论在老年痴呆症患者临床护理中的应用效果,为临床护理提供参考。方法:选择2012年3月至2014年3月我院收治的老年痴呆患者200例,随机分为治疗组和对照组。对照组采用常规护理措施,治疗组采用华生关怀理论进行干预。分别于干预前后采用简易智能量表(MMSE)、蒙特利尔认知评估量表(MOCA)、AD评定量表认知部分(ADAS-Cog)、日常生活活动量表(ADL)、中医症状积分量表对两组患者进行测评。结果:与干预前比较,两组患者干预后的MMSE和MOCA评分显著升高,ADAS-Cog、ADL和中医症状积分明显降低,差异具有统计学意义(P0.05);与对照组比较,治疗组患者变化更明显(P0.01)。两组患者干预前后的血尿常规、肝肾功能及心电图等指标无显著差异(P0.05)。结论:利用华生关怀理论护理老年痴呆症患者,不仅能改善患者的病情,缓解心理压力,而且有利于减轻家庭和社会负担。     

Stacking geometry for non‐canonical G:U wobble base pair containing dinucleotide sequences in RNA: dispersion‐corrected DFT‐D study

Emergence of thousands of crystal structures of noncoding RNA molecules indicates its structural and functional diversity. RNA function is based upon a large variety of structural elements which are specifically assembled in the folded molecules. Along with the canonical Watson‐Crick base pairs, different orientations of the bases to form hydrogen‐bonded non‐canonical base pairs have also been observed in the available RNA structures. Frequencies of occurrences of different non‐canonical base pairs in RNA indicate their important role to maintain overall structure and functions of RNA. There are several reports on geometry and energetic stabilities of these non‐canonical base pairs. However, their stacking geometry and stacking stability with the neighboring base pairs are not well studied. Among the different non‐canonical base pairs, the G:U wobble base pair (G:U W:WC) is most frequently observed in the RNA double helices. Using quantum chemical method and available experimental data set we have studied the stacking geometry of G:U W:WC base pair containing dinucleotide sequences in roll‐slide parameters hyperspace for different values of twist. This study indicates that the G:U W:WC base pair can stack well with the canonical base pairs giving rise to large interaction energy. The overall preferred stacking geometry in terms of roll, twist and slide for the eleven possible dinucleotide sequences is seen to be quite dependent on their sequences. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 328–338, 2015.     

A Report of the James Watson Lecture at Yale University

In March 2012, Nobel Prize winner James Watson gave a seminar at Yale University entitled “Driven by Ideas.” In his lecture, Watson discussed his personal vision for the future of science, specifically addressing how the scientific community should approach developing anticancer agents. He discussed the use of glycolytic inhibitors as anticancer agents due to the Warburg effect, as well as the benefits of metformin and anti-inflammatory drugs to help prevent cancer. He also compared drugs that target cell proliferation instead of targeting cell growth. Additionally, Watson commented on the mechanisms for how research should be conducted in the laboratory.     

Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender

Cisplatin (cis-diamminedichloroplatinum) is a common chemotherapeutic drug that reacts with the N7 atoms of adjacent guanines in DNA to form the Pt-1,2-d(GpG) intrastrand cross-link (Pt-GG), a major product to block DNA replication. Translesion DNA synthesis has been implicated in chemoresistance during cisplatin treatment of cancer due to Pt-GG lesion bypass. Gene knockdown studies in human cells have indicated a role for polκ during translesion synthesis of the Pt-GG lesion. However, the bypass activity of polκ with cisplatin lesions has not been well characterized. In this study, we investigated polκ's ability to bypass Pt-GG lesion in vitro and determined two crystal structures of polκ in complex with Pt-GG DNA. The ternary complex structures represent two consecutive stages of lesion bypass: nucleotide insertion opposite the 5′G (Pt-GG2) and primer extension immediately after the lesion (Pt-GG3). Our biochemical data showed that polκ is very efficient and accurate in extending DNA primers after the first G of the Pt-GG lesion. The structures demonstrate that the efficiency and accuracy is achieved by stably accommodating the bases with the cisplatin adduct in the active site for proper Watson–Crick base pairing with the incoming nucleotide in both the second insertion and post-insertion complexes. Our studies suggest that polκ works as an extender for efficient replication of the Pt-GG lesion in cells. This work holds promise for considering polκ, along with polη, as potential targets for drug design, which together could improve the efficacy of cisplatin treatment for cancer therapy.     

Vegetation succession in lakes of West Connemara,Ireland: comparing predicted and actual changes

Abstract. Changes in the vegetation of lakes and wetlands were investigated over a period of 18 years. It was assumed that changes in vegetation were related to changes in agricultural land use resulting in increased phosphate levels in surface waters. Data were collected in 1975, 1988 and 1993. Multivariate techniques were used to relate changes in vegetation to changes in environmental factors. With the use of a Markovian chain model, vegetation development was projected into the future. Projections based on vegetation dynamics between 1975 and 1988 were compared with actual changes in the vegetation. The vegetation dynamics appeared stable on a regional scale but quite dynamic on a local scale. A continuous decline in species diversity was noted as well as an overall increase of phosphate level. However, only minor changes in vegetation could be attributed to this increase of phosphate. Major changes were a result of fluctuations in water level. These changes coincide with periods of drier and wetter climate. Because of the fluctuating nature of these changes, predicted vegetation change did deviate from the observed change.     

Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research

As of today, a great amount of experimental and theoretical phenomenological data have been collected in the literature according the mutagenic action of the classical mutagen – 2-aminopurine (2AP). However, so far they have not received proper explanation and substantiation. In this Opinion Piece, we provide an overview of recent progress in computational design and modeling of the physico-chemical mechanisms of the mutagenic action of 2AP. Results of quantum-chemical studies, aimed at the elucidation of the key microstructural mechanisms of the mutagenicity of 2AP, have been summarized here. In this context, for the first time it was outlined the most important surveys: Why 2AP is incorporated into DNA in trace concentrations? Whether classical mechanisms presented in the literature according the formation of the rare tautomers of canonical DNA bases work also for base analogue – 2AP? In what way 2AP induces replication and incorporation errors? Whether the amino-imino tautomerisation of 2AP is related to its mutagenicity, that is whether the 2AP* rare tautomer is mutagenic? It is emphasized that the applied approach has a proper theoretical substantiation, since it is based on our microstructural theory of the spontaneous point mutagenesis in DNA, and at the same time it accumulates scenarios of the origin of the induced point errors – transitions and transversions, which the classical Watson–Crick tautomeric hypothesis permits. Moreover, using author’s methodology, the profiles of the main physico-chemical characteristics for the tautomerisation reactions involving 2AP, which are integral parts of the biologically important tautomerically-conformational transformations, have been presented. Obtained results open new perspectives for prediction and design of the mutagenic derivatives of the nucleotide bases of any structure and origin before their synthesis and also for planning of new experiments and interpretation of the existing data. Abbreviations 2AP 2-Aminopurine

A adenine

C cytosine

DPT double proton transfer

G guanine

IRC intrinsic reaction coordinate

KP key point

T thymine

w wobble

WC Watson–Crick

vdW van der Waals

H-bond hydrogen bond

Communicated by Ramaswamy H. Sarma     

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs

Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non‐canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte‐Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER‐parm99bsc0 and CHARMM‐36 force‐fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte‐Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson–Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non‐canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse‐grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson–Crick base pairs, as found often in the non‐coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212–226, 2016.