Ageing and longevity in the Decapoda (Crustacea): A review

Ageing and longevity is a neglected field of crustacean biology. Information on longevity is available for less than 2% of the extant species of the Decapoda. Maximum ages reliably determined range from 40 days to 72 years corresponding to a life span difference of a factor of 650. The shortest-lived decapods are planktonic dendrobranchiate shrimps, and particularly long-lived species with life spans of decades are found in the Astacidea. Most decapods seem to live for 1-10 years. High geographical latitude, the deep sea and freshwater caves promote longevity. The majority of the Decapoda is indeterminately growing and presumably characterized by negligible senescence. The adults of the determinately growing decapods like some brachyuran crabs suffer from mechanical senescence and are unable to regenerate lost appendages. The decapod crustaceans have developed many effective anti-ageing mechanisms including moulting, detoxification of free radicals, removal of cellular waste, renewal of tissues by life-long stem cell activity, regeneration of appendages, detoxification of environmental pollutants and isolation of pathogens and diseased tissue areas by melanisation and encapsulation. Age related diseases including cancer are virtually unknown. The present compilation of data on longevity and senescence in decapods is the first one that covers the whole spectrum of a higher invertebrate taxon. It is hoped to provide an interesting source of information for carcinologists and biogerontologists. Further improvement of knowledge on ageing and longevity in the Decapoda would be beneficial for crustacean aquaculture, fisheries and ecological modelling. Some decapods even have good potential to become models for general ageing research.     

Describing Values in Relation to Choices in LCA (7 pp)

Intention, Goal, Scope, Background It has gained growing acceptance in recent years that there are values in LCA, and several authors have discussed how value orientations can influence LCA models and results. The aim of this article is to continue this discussion and to focus on value choices in LCA. Objectives To find a way of describing value orientations in relation to choices in LCA. Methods This objective has been pursued in this paper by investigating the relationship between values and traditional science, exploring the concept of values, investigating the relationship between values and choice, and suggesting a way to describe the value base for specific choices in LCA. Results and Discussion Research on how to improve the environmental performance of products resembles peace research in that it aims to achieve a certain value-laden situation in society. The epistemological basis for peace research also seems to apply to LCA research. The term value has many meanings. There are several classification methods for values and I claim that one is more suitable for choices in LCA than the others. The correlation between values and choice is not straightforward, and values can only partially explain choices. Conclusions Describing the value base for choices in LCA increases the consistency and transparency of the value choices and offers a means of justifying them. Recommendations and Outlook It is recommended that the value base is described in terms of 1) what is included in the concern for the environment 2) how tradeoffs are made and 3) how uncertainty is handled.     

Turkish nationalism and the Kurdish question

This article addresses the ways in which Turkish nationalism has perceived the Kurdish question. It is shown that both Turkish nationalism and the Kurdish question have passed through some paradigmatic moments in the twentieth century. This, I argue, has shaped the way that the Kurdish question has been perceived by Turkish nationalism. While the Kurdish question had been seen by Turkish nationalism mostly in terms of a fatal rivalry between the backward, pre-modern and tribal past and the prosperous present in the first half of the century, it was perceived in terms of a tension between the peripheral economy and national market in the fifties and sixties. In the 1970s, the Kurdish unrest was believed to be a product of communist incitement. Despite this impurity in perception, one thing has remained nearly unchanged for Turkish nationalism: Kurds could become Turkish. In other words, Turkish nationalism of the republican era has principally perceived Kurds as future-Turks. However, the signs in circulation at present indicate that the confidence of Turkish nationalism as to Kurds’ potential of becoming Turkish is not as firm as it used to be. At present, Turkish nationalism seems to be getting prepared to abandon its contention that Kurds are future-Turks.     

A critical note on ‘exclusive recognition’

Cenk Saracoglu conceptualizes the antipathy towards Kurdish migrants manifesting in certain cities of Turkey since the early 2000s as ‘exclusive recognition’ in his article ‘“Exclusive recognition”: the new dimensions of the question of ethnicity and nationalism in Turkey’ published in Ethnic and Racial Studies 32(4). According to the author, these recent developments represent ‘a historically specific ethnicization process’ and its sources cannot be found directly and only in historical discourses and policy of mainstream Turkish nationalism. In this note, I contradict the author's claims by asserting that the recent manifestations of anti-Kurdish sentiments are an extension of the ongoing policies of Turkish national identity based on Turkish nationalism.     

The self-morningness/eveningness (Self-ME): An extremely concise and totally subjective assessment of diurnal preference

The assessment of diurnal preference, or the preferred timing of sleep and activity, is generally based on comprehensive questionnaires such as the Horne–Östberg (HÖ). The aim of the present study was to assess the reliability of a subject’s self-classification as extremely morning (Self-MM), more morning than evening (Self-M), more evening than morning (Self-E) or extremely evening (Self-EE) type, based on the last question of the HÖ (Self-ME). A convenience sample of 461 subjects [23.8?±?4.7 years; 322 females] completed a full sleep–wake assessment, including diurnal preference (HÖ), night sleep quality (Pittsburgh Sleep Quality Index, PSQI), daytime sleepiness (Karolinska Sleepiness Scale, KSS), and habitual sleep–wake timing (12?d sleep diaries; n?=?296). Significant differences in HÖ total score were observed between Self-ME classes, with each class being significantly different from neighboring classes (p?<?0.0001). Significant differences in sleep–wake timing (bed time, try to sleep and sleep onset, wake up, and get up time) were observed between Self-ME classes. Such differences were maintained when sleep–wake habits were analysed separately on work and free days, and also in a smaller group of 67 subjects who completed the Self-ME as a stand-alone rather than as part of the original questionnaire. Significant differences were observed in the time-course of subjective sleepiness by Self-ME class in both the large and the small group, with Self-MM and Self-M subjects being significantly more alert in the morning and sleepier in the evening hours compared with their Self-E and Self-EE counterparts. Finally, significant differences were observed in night sleep quality between Self-ME classes, with Self-EE/Self-E subjects sleeping worse than their Self-MM/Self-M counterparts, and averaging just over the abnormality PSQI threshold of 5. In conclusion, young, healthy adults can define their diurnal preference based on a single question (Self-ME) in a way that reflects their sleep–wake timing, their sleepiness levels over the daytime hours, and their night sleep quality. Validation of the Self-ME across the decades and in diseased populations seems worthy.     

Good student questions in inquiry learning

Acquisition of scientific reasoning is one of the big challenges in education. A popular educational strategy advocated for acquiring deep knowledge is inquiry-based learning, which is driven by emerging ‘good questions’. This study will address the question: ‘Which design features allow learners to refine questions while preserving student ownership of the inquiry process?’ This design-based research has been conducted over several years with advanced high-school biology classes. The results confirm the central role of question elaboration as an interactive process that leads from vague to complex and adequate. To make this happen, the inquiry process must extend over a long time, learners and teachers should share a knowledge improvement goal, and text produced by students should be structured by question–answer pairs addressing a single concept using authentic resources. Further features are discussion with peers, teacher feedback with respect to answer elaboration and conceptual differentiation, and finally, teacher guidance that should fade out in successive inquiry cycles to ensure student responsibility.     

Studies On The Cross Strand Hydrogen Bonds In DNA Double Helices

Abstract

A systematic analysis has been carried out to examine all the stereochemically possible bifurcated hydrogen bonds including those of cross strand type between propeller twisted base pairs in DNA double helices by stereochemical considerations involving base pairs alone and by molecular mechanics studies on dimer and trimer duplexes. The results show that there are limited number of combinations of adjacent base pairs that would facilitate bifurcated cross- strand hydrogen bond (CSH). B-type helices concomitant with negative propeller twist seem to be more favored for the occurrence of CSH than canonical A-type helices because of slide in the latter. The results also demonstrate that helices with appropriate sequences may possess continuous run of these propeller twist driven cross strand hydrogen bonds indicating that they may infact be considered as yet another general structural feature of DNA helices.     

High throughput preparation of fly genomic DNA in 96-well format using a paint-shaker

Sample homogenization is an essential step for genomic DNA extraction, with multiple downstream applications in Molecular Biology. Genotyping hundreds or thousands of samples requires an automation of this homogenization step, and high throughput homogenizer equipment currently costs 7000 euros or more. We present an apparatus for homogenization of individual Drosophila adult flies in 96-well micro-titer dishes, which was built from a small portable paint-shaker (F5 portable paint-shaker, Ushake). Single flies are disrupted in each well that contains extraction buffer and a 4-mm metal ball. Our apparatus can hold up to five 96-well micro-titer plates. Construction of the homogenizer apparatus takes about 3–4 days, and all equipment can be obtained from a home improvement store. The total material cost is approximately 700 euros including the paint-shaker. We tested the performance of our apparatus using the ZR-96 Quick-gDNA? kit (Zymo Research) homogenization buffer and achieved nearly complete tissue homogenization after 15 minutes of shaking. PCR tests did not detect any cross contamination between samples of neighboring wells. We obtained on average 138 ng of genomic DNA per fly, and DNA quality was adequate for standard PCR applications. In principle, our tissue homogenizer can be used for isolation of DNA suitable for library production and high throughput genotyping by Multiplexed Shotgun Genotyping (MSG), as well as RNA isolation from single flies. The sample adapter can also hold and shake other items, such as centrifuge tubes (15–50 mL) or small bottles.     

eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth

Referring to European history of natural sciences as an example, I discuss the relation between development of standards and the emergence of new epistemic virtues. I distinguish standards relating to scientific argumentation from standards relating to data production. The former are based on truth-seeking epistemic virtues and use criteria of logical coherence and empirical grounding. They are important for the justification of an explanatory hypothesis. Data and metadata standards, on the other hand, concern the data record itself and all steps and actions taken during data production and are based on virtues of objectivity. In the second part I focus on data and metadata standards and argue that, in order to meet the requirements of eScience, the specification of the currently popular minimum information checklists should be complemented to cover four aspects: (i) content standards, which increase reproducibility and operational transparency of data production, (ii) concept standards, which increase the semantic transparency of the terms used in data records, (iii) nomenclatural standards, which provide stable and unambiguous links between the terms used and their underlying definitions or their real referents, and (iv) format standards, which increase compatibility and computer-parsability of data records. I discuss the role of scientific terminology for standardizing data and the need for using semantically standardized and formalized data-reporting languages in the form of controlled vocabularies and ontologies for establishing content standards for data in the life sciences. Finally I comment on the necessity of community participation in the development and application of standards and in making data openly available.     

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.