Phytoserological contribution to the systematic placement of the Typhales

Serological methods were used to compare the major storage seed proteins, the legumin-like proteins, from the Typhales with other monocot taxa to obtain a more complete understanding of the phylogenetic relationships of the Typhales. Both reference taxa, Typha latifolia and Sparganium erectum were found to be serologically very similar and reveal the close relationship of the Typhaceae and Sparganiaceae and should best be placed in a common order Typhales. Furthermore, the data indicate a close phylogenetic relationship between the Typhales and the wind pollinated Pandaniflorae and also the animal pollinated Zingiberiflorae. Additionally, relationships to the Commeliniflorae (Juncales, Cyperales, Poales) as well as towards the Asparagales (especially the xeromorphic Agavaceae) are indicated. In phylogeny, a branch from pro-Asparagales is postulated leading to the Zingiberiflorae and at least diphyletically to the wind pollinated Pandanaceae plus Typhales and to the Commeliniflorae.     

A systematic survey of centrality measures for protein-protein interaction networks

Background

Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

Results

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

Conclusions

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

     

A survey on the intraclear inclusions in the Schrophulariaceae and their systematic significance

A survey of nuclear inclusions in chlorenchyma cells is given for 290 taxa of the Scrophulariaceae, covering 72 genera; 172 are new data and the remainder are from previous reports by the author. In addition to the 5 types of nuclear inclusions already determined by their different ultrastructural morphology — amorphous (A), lamellar (L), fibrillar (F), tubular (T), and crystalline (C) — and to subtypes C2, three new subtypes — A2, L2, T2 - specific to certain genera or small groups of genera are reported. These new subtypes are described in detail and their distribution in the family discussed. Although the proteinic nature was unquestionably demonstrated, the origin and function of plant nuclear inclusions is far from being understood. In the Scrophulariaceae they have been recognized in 242 out of 290 taxa studied (83.4%), in a total of 60 out of 72 genera (83.3%). On the basis of the occurrence and qualitative distribution of the nuclear inclusions, the family can be subdivided into four main group: 1) with lamellar inclusions, 2) with amorphous inclusions, 3) with inclusions other than those in the two former groups, and 4) with no nuclear inclusions. The relationship between the distribution on the nuclear inclusions throughout the family and the current systematic arrangement into subfamilies are analyzed and the transfer of some genera to different tribes or to a tribe of their own is proposed, e.g., in the case of Mimulus, Leucocarpus, Halleria, Russelia, Angelonia, Rehmannia , and Campylanthus . Finally, a possible evolutionary trend of the different types of nuclear inclusions based on their structural complexity and on the occurrence in allied families is offered.     

Abundance-related systematic bias in the quantification of phenology using site presence-based survey methods

Reliable quantification of the timing of spring phenology is important to the understanding of ecological responses to climate change. Citizen science data have a potentially useful role supporting these types of studies. Site presence-based methods represent a relatively simple means of following spring phenology, including migrant bird arrival. However, binary presence/absence observations are ill-suited to following the build-up of individuals during the spring emergence or arrival period because presence may be detected uniformly after a small proportion only of the population is present. The reliability of this survey method has been evaluated by mathematical modelling, further supported by comparison of model predictions with arrival date estimates determined in previous field studies. Modelling demonstrates a systematic abundance-dependent bias in median arrival dates estimated using site presence-based survey methods in which the apparent distribution is shifted increasingly ahead of the true distribution with increasing abundance, a feature also evident in field observations. Since this error in the estimate changes with abundance, abundance changes with time will lead to a distorted picture of the phenological trend with time, impacting on the reliability of these methods for characterizing phenological events. The model provides a general framework for identifying when this inherent bias will arise, and for compensating for it by reference to count data obtained from other sources, thereby assisting in the provision of improved estimates of phenological change. To ensure that the most appropriate conclusions concerning phenological change are drawn from studies using site presence data, it is imperative that these identified methodological limitations are recognized and properly considered during data interpretation.     

鸟撞建筑现象概述及系统性调查案例分析

随着城市化进程的推进, 各类人造设施, 尤其是建筑物及建筑物上的玻璃, 已经成为鸟类生存的重要威胁。有些建筑物及其上的玻璃拥有透明和反光的特性, 这样的特性令鸟类无法辨认出玻璃的存在, 导致在飞行途中与玻璃相撞致死, 或致伤、致残。这样的现象被称为鸟撞建筑或鸟撞建筑玻璃, 简称鸟撞。在北美, 针对鸟撞现象的研究较多。在美国, 鸟撞每年造成3-10亿只鸟死亡, 是人类活动直接造成的鸟类死亡中最突出的原因之一。然而, 目前中国对于鸟撞的研究和关注还非常有限。随着中国对城市生态学和城市生物多样性的重视, 鸟撞现象也应进入到生物多样性研究与保护的视野中。为了让该议题被更多人所了解, 本综述总结和介绍了鸟撞现象, 包括影响鸟撞发生的因素、预防鸟撞措施的进展和鸟撞调查的方法概述。此外, 本文以案例形式介绍了国内首个系统性鸟撞建筑的调查, 并阐释了该类调查的可行性与必要性。基于过往研究, 本文最后提出了针对未来鸟撞建筑研究方向的建议: (1)对中国鸟撞建筑现象进行整体评估; (2)建立系统性调查方法和鸟撞数据收集的系统; (3)进一步探究鸟撞机理; (4)促进和改变公众意识、影响城市规划与建筑革新。     

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).     

A systematic survey of in vivo obligate chaperonin‐dependent substrates

Chaperonins are absolutely required for the folding of a subset of proteins in the cell. An earlier proteome‐wide analysis of Escherichia coli chaperonin GroEL/GroES (GroE) interactors predicted obligate chaperonin substrates, which were termed Class III substrates. However, the requirement of chaperonins for in vivo folding has not been fully examined. Here, we comprehensively assessed the chaperonin requirement using a conditional GroE expression strain, and concluded that only ～60% of Class III substrates are bona fide obligate GroE substrates in vivo. The in vivo obligate substrates, combined with the newly identified obligate substrates, were termed Class IV substrates. Class IV substrates are restricted to proteins with molecular weights that could be encapsulated in the chaperonin cavity, are enriched in alanine/glycine residues, and have a strong structural preference for aggregation‐prone folds. Notably, ～70% of the Class IV substrates appear to be metabolic enzymes, supporting a hypothetical role of GroE in enzyme evolution.     

Reporting of adverse drug reactions in randomised controlled trials – a systematic survey

Background  

Decisions on treatment are guided, not only by the potential for benefit, but also by the nature and severity of adverse drug reactions. However, some researchers have found numerous deficiencies in trial reports of adverse effects. We sought to confirm these findings by evaluating trials of drug therapy published in seven eminent medical journals in 1997.     

NAR Breakthrough Article: A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Cys₂His₂ zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain''s well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain–DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain–DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.     

A systematic survey on the diagnosis strategy and patient management of type 1 diabetes by Chinese physicians

The qualification of physicians is a key factor in controlling type 1 diabetes(T1 D) since they provide crucial information to their patients about self-management. To investigate whether Chinese physicians' medical strategies influence the control of T1 D in their patients, we designed a questionnaire to survey Chinese physicians, which covered their diagnosis and patient-management strategies for T1 D. A total of 442 completed questionnaires were received from 35 public hospitals in 12 cities. The results showed Chinese physicians mainly diagnosed T1 D based on the clinical features and islet dysfunction. One-third of physicians in this study still prescribed non-basal-bolus insulin regimens to their T1 D patients. More than 80% of the doctors prescribed alpha-glucosidase inhibitors as adjunctive therapy, in addition to insulin therapy. Moreover, most of the physicians in China did not pay attention to identify coexistent autoimmune diseases. T1 D patients in China were not armed with self-management knowledge and skills, which should be provided by their doctors. One of the circumstances leading to insufficient disease control in Chinese T1 D patients is the ineffective therapeutic strategy prescribed by their physicians. We need to promote knowledge of efficient strategies among physicians in China to achieve better disease control in Chinese T1 D patients in the future.     

Taxonomic gap in wood-inhabiting fungi: identifying understudied groups by a systematic survey

Despite advances in phylogenetic research and the number of ecological studies focusing on wood-inhabiting fungi, these species still represent a taxonomically poorly known group of organisms. In this study, our overall aim was to detect and characterize the understudied wood-inhabiting fungal groups in the beech forests of Navarre (northern Spain). We present a list of 326 wood-inhabiting fungal species, out of which 36 % are first regional records. Comparing the already recorded fungal species in this territory and the list of firstly recorded species, we found that field-mycologists tend to focus on certain fungal groups, and in general rare species are less frequently encountered. Particularly, species with corticioid fruit body type have been especially overlooked in this territory. We attribute the high proportion of new regional records to the use of a systematic sampling design.     

Flavonoid chemistry ofPolygonum sect.Tovara (Polygonaceae): A systematic survey

Polygonum sect.Tovara includes three controversial species;P. virginianum, P. filiforme, andP. neofiliforme. The flavonoid chemistry of these was examined to provide additional information on their delimitation and levels of differentiation. Eight flavonoid compounds were isolated and identified, all of which were 3-O-glycosides of the flavonols kaempferol, quercetin, and myricetin, and their acylated derivatives. Although they exhibit relatively simple flavonoid profiles, the three taxa are readily distinguished by their flavonoid constituents. In addition, they show fundamental differences in flavonol types and glycosylation patterns. These results, in conjunction with evidence from the morphology, strongly suggest thatP. virginianum, P. filiforme, andP. neofiliforme are closely allied but distinct species.     

Reporting of noninferiority and equivalence randomized trials for major prostaglandins: A systematic survey of the ophthalmology literature

Aims

Implantable defibrillators are considered life-saving therapy in heart failure (CHF) patients. Surprisingly, the recent Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT) reached an opposing conclusion from that of numerous other trials about their survival benefit in patients with advanced CHF. A critical analysis of common control trial design may explain this paradoxical finding, with important implications for future studies.

Methods and Results

Common control trials compare several intervention groups to a single rather than separate control groups. Though potentially requiring fewer patients than trials using separate controls, variation in the common control group will influence all comparisons and creates correlations between findings. During subgroup analyses, this dependency of outcomes may increase belief in the presence of a real subgroup effect when, in fact, it should increase skepticism. For example, a high (r = 0.92), statistically unlikely (p = 0.052) correlation between comparisons was observed across the subgroups reported in SCD-HeFT. Such concordance between amiodarone and a defibrillator across subgroups was unexpected, given how much the effects of these treatments significantly differed from one another in the main study. This suggests the study's subgroup findings (specifically the absence of benefit from defibrillators in advanced CHF) were not necessarily a consequence of treatment; more likely, they resulted from variation in what the treatments were compared against, the common control.

Conclusion

Common control trials can be more efficient than other designs, but induce dependence between treatment comparisons and require cautious interpretation.     

Research questions and priorities for tuberculosis: a survey of published systematic reviews and meta-analyses

Background

Systematic reviews are increasingly informing policies in tuberculosis (TB) care and control. They may also be a source of questions for future research. As part of the process of developing the International Roadmap for TB Research, we did a systematic review of published systematic reviews on TB, to identify research priorities that are most frequently suggested in reviews.

Methodology/Principal Findings

We searched EMBASE, MEDLINE, Web of Science, and the Cochrane Library for systematic reviews and meta-analyses on any aspect of TB published between 2005 and 2010. One reviewer extracted data and a second reviewer independently extracted data from a random subset of included studies. In total, 137 systematic reviews, with 141 research questions, were included in this review. We used the UK Health Research Classification System (HRCS) to help us classify the research questions and priorities. The three most common research topics were in the area of detection, screening and diagnosis of TB (32.6%), development and evaluation of treatments and therapeutic interventions (23.4%), and TB aetiology and risk factors (19.9%). The research priorities determined were mainly focused on the discovery and evaluation of bacteriological TB tests and drug-resistant TB tests and immunological tests. Other important topics of future research were genetic susceptibility linked to TB and disease determinants attributed to HIV/TB. Evaluation of drug treatments for TB, drug-resistant TB and HIV/TB were also frequently proposed research topics.

Conclusions

Systematic reviews are a good source of key research priorities. Findings from our survey have informed the development of the International Roadmap for TB Research by the TB Research Movement.     

A systematic survey for thermophilic fermentative bacteria and archaea in high temperature petroleum reservoirs

Abstract: Production waters from 36 high temperature petroleum reservoirs were examined for the presence of thermophilic, fermentative microorganisms. The direct supplementation of production waters with glucose and either yeast extract, peptone, tryptone or casamino acid resulted in the isolation of thermophilic, fermentative microorganisms from 47% of the petroleum reservoirs examined. Three distinctive morphological groups were isolated from the production waters of petroleum reservoirs with depths ranging from 396–3048 metres, temperatures ranging from 21–130°C, salinities ranging from 2.8–128 gl⁻¹ and pHs ranging from 6.0–8.5. Group 1 were pleomorphic rod-shaped bacteria, Group 2 were sheathed rod-shaped bacteria, and Group 3 were coccoid archaea. Partial characterisation of strains from one seawater-flooded petroleum reservoir and three non-waterflooded petroleum reservoirs tentatively identified some strains in Group 1 as members of the genera Thermoanaerobacter and Thermoanaerobacterium , Group 2 as members of the Thermotogales order, and Group 3 as members of the genus Thermococcus . Production water salinity determined the type of microorganisms that were isolated. Group 1 organisms were found primarily in petroleum reservoirs with salinities less than 30 g/l, while Group 2 and 3 organisms were found to dominate in more saline reservoirs. The successful isolation of thermophilic, fermentative microorganisms from petroleum reservoirs decreased significantly with increasing salinity and temperature. These findings support the existence of a deep biosphere where fermentative microorganisms are widespread.