Joker: An algorithm to insert patterns into sequences for designing antimicrobial peptides

Innovative alternatives to control bacterial infections are need due to bacterial resistance rise. Antimicrobial peptides (AMPs) have been considered as the new generation of antimicrobial agents. Based on the fact that AMPs are sequence-dependent, a linguistic model for designing AMPs was previously developed, considering AMPs as a formal language with a grammar (patterns or motifs) and a vocabulary (amino acids). Albeit promising, that model has been poorly exploited mainly because thousands of sequences need to be generated, and the outcome has high similarity to already known AMPs. Here we present Joker, an innovative algorithm that improves the application of the linguistic model for rational design of antimicrobial peptides. We modelled the AMPs as a card game, where Joker combines the cards in the hand (patterns) with the cards in the table (sequence templates), generating a few variants. Our algorithm is capable of improving existing AMPs or even creating new AMPs from inactive peptides. A standalone version of Joker is available for download at <http://github.com/williamfp7/Joker> and requires a Linux 32-bit machine.     

镇痛指数在全麻手术中评估镇痛程度的临床价值

目的：探讨脑电镇痛指数（PRi）评估全身麻醉手术中镇痛程度的临床价值,为临床应用提供理论依据。方法：ASAI-Ⅱ级,拟于全身麻醉下行经腹手术的病人20例。患者入手术室后持续有创监测收缩压（SBP）、舒张压（DBP）、心率（HR）,实时监测脑电双频指数（BIS）和镇痛指数（PRi）。于麻醉诱导后气管插管前,气管插管后1 min、切皮前、切皮后2 min、追加芬太尼前,追加芬太尼5 min后记录BIS、PRi、SBP、DBP、HR的变化。结果：气管插管和切皮均引起SBP、DBP、HR的显著升高（P<0.05）;追加芬太尼后SBP、DBP、HR均降低（P<0.05）。气管插管和切皮均未引起BIS的显著变化（P>0.05）;追加芬太尼后BIS有所下降（P<0.05）。气管插管和切皮均引起PRi的显著升高（P<0.05）;追加芬太尼后PRi降低（P<0.05）。气管插管和切皮均引起SBP、DBP、HR、PRi的显著升高（P<0.05）,但均未引起BIS的显著变化（P>0.05）;追加芬太尼后SBP、DBP、HR、BIS和PRi均明显降低（P<0.05）。结论：在丙泊酚联合瑞芬太尼全身麻醉手术中,PRi能够反映伤害性刺激的变化,与伤害性刺激过程一致,对全身麻醉中镇痛程度的评估有指导意义。     

Sea ice meiofauna distribution on local to pan‐Arctic scales

Arctic sea ice provides microhabitats for biota that inhabit the liquid‐filled network of brine channels and the ice–water interface. We used meta‐analysis of 23 published and unpublished datasets comprising 721 ice cores to synthesize the variability in composition and abundance of sea ice meiofauna at spatial scales ranging from within a single ice core to pan‐Arctic and seasonal scales. Two‐thirds of meiofauna individuals occurred in the bottom 10 cm of the ice. Locally, replicate cores taken within meters of each other were broadly similar in meiofauna composition and abundance, while those a few km apart varied more; 75% of variation was explained by station. At the regional scale (Bering Sea first‐year ice), meiofauna abundance varied over two orders of magnitude. At the pan‐Arctic scale, the same phyla were found across the region, with taxa that have resting stages or tolerance to extreme conditions (e.g., nematodes and rotifers) dominating abundances. Meroplankton, however, was restricted to nearshore locations and landfast sea ice. Light availability, ice thickness, and distance from land were significant predictor variables for community composition on different scales. On a seasonal scale, abundances varied broadly for all taxa and in relation to the annual ice algal bloom cycle in both landfast and pack ice. Documentation of ice biota composition, abundance, and natural variability is critical for evaluating responses to decline in Arctic sea ice. Consistent methodology and protocols must be established for comparability of meiofauna monitoring across the Arctic. We recommend to (1) increase taxonomic resolution of sea ice meiofauna, (2) focus sampling on times of peak abundance when seasonal sampling is impossible, (3) include the bottom 30 cm of ice cores rather than only bottom 10 cm, (4) preserve specimens for molecular analysis to improve taxonomic resolution, and (5) formulate a trait‐based framework that relates to ecosystem functioning.     

Oat residue and soil compaction influences on common root rot (Aphanomyes euteiches) of peas in a fine-textured soil

Management of common root rot (Aphanomyces euteiches Drechs.) in peas (Pisum sativum L.) is sought primarily by host crop avoidance for several years. Soil compaction is known to aggravate A. euteiches disease in peas but effects on infection and subsequent symptom development are not sufficiently known to assist in cultural control. Several isolated observations have noted that oat crop residues may suppress A. euteiches infection and disease in pea roots. The individual and combined influence (a factorial combination of two factors each at two levels) of a prior oat crop and soil compaction were studied for their effects on common root rot severity in processing peas grown in an A. euteiches disease nursery on a fine-textured soil in the northern Corn Belt of the USA. A previous crop of summer oats relative to prior-year peas significantly suppressed common root rot and increased pea fresh vine weight 210% at peak bloom stage. Both fresh vine weight and green pea yield were reduced as much as 63% by soil compaction and increased as much as 48% by a prior oat crop. Greater soil bulk density at the 10 to 25-cm depth identified wheel traffic compaction patterns in each year. A 10-fold reduction of saturated hydraulic conductivity in the 10 to 25-cm compacted zone and high soil-water potentials within the upper 60 cm both confirmed an impaired water drainage, especially during infiltration events. These observations support the use of a previous full season or summer oat crop jointly with chisel plowing, plus the prevention of excessive traffic during secondary tillage and planting, to reduce common root rot in a field infested with A. euteiches. Shallow incorporation of oat shoot and root residue by chiseling could be a crucial component of the cultural control of the disease. R Rodriguez Kabana Section editor     

Structure and development of the ctenial spines on the scales of a teleost fish,the cichlid Cichlasoma nigrofasciatum

Sire, J.‐Y. and Arnulf, I. 2000. Structure and development of the ctenial spines on the scales of a teleost fish, the cichlid Cichlasoma nigrofasciatum. — Acta Zoologica (Stockholm) 81 : 139–158 Numerous teleost species possess ctenoid scales characterized by the presence of ctenial spines arranged in rows (the cteni) along their posterior, free margin. Whilst the morphology and function of the ctenial spines are similar to those of odontodes (extra‐oral teeth), e.g. in armored catfish, their homology is questionable. To address this problem, we have studied ctenial spine development, structure, attachment to a bony support, and replacement with the aim of comparing these features to those described for odontodes. The ctenial spines have been studied in a growth series of the cichlid Cichlasoma nigrofasciatum, using light, scanning and transmission electron microscopy. Ctenial spines are entirely constituted of a collagen matrix. They lack a pulp cavity and, although their distal end can be in contact with the epidermal basal layer cells, they are not covered by an enameloid‐like tissue. They are attached to the scale by means of a narrow strand of unmineralized collagen matrix acting as a ligament and allowing spines to be movable. The ctenial spines develop as prolongations of the external layer of the scale, a woven‐fibroid collagen matrix, and subsequently grow by addition of parallel‐fibred collagen matrix. New ctenial spines are added at the posterior scale border in waves that follow the same rhythm as the deposition of circuli in the anterior region. From the focus region to the scale border, the ctenial spines constitute lines in which only the most posterior ctenial spine is functional. The other spines that are no longer functional are not shed but resorbed from the top, and their attachment region mineralizes and thickens by deposition of new material. The remnants of spines constitute the main part of the superficial layer of the scale in which anchoring bundles attach; this region is covered afterwards by the limiting layer, a tissue devoid of collagen fibrils. Because of their tooth‐like morphology (shape and size), their posterior orientation and their attachment to the scale surface, the ctenial spines resemble odontodes. Moreover, both elements perform a similar hydrodynamic function. Nevertheless, the structure and development of the ctenial spines differ completely from those of odontodes and consequently, they cannot be considered homologous elements. Ctenial spines and odontodes in teleosts provide us with a beautiful example of homoplasy; they share shape and function, but have a different origin as evidenced by their different structure and process of development.     

Continent‐scale global change attribution in European birds ‐ combining annual and decadal time scales

Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader foundation for attributing species responses to global change may be achieved by complementing an attributes‐based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we investigate the recent impact of multiple environmental changes on European farmland birds, here focusing on climate change and land use change. We analyze more than 800 time series from 18 countries spanning the past two decades. Analysis of long‐term population growth rates documents simultaneous responses that can be attributed to both climate change and land‐use change, including long‐term increases in populations of hot‐dwelling species and declines in long‐distance migrants and farmland specialists. In contrast, analysis of annual growth rates yield novel insights into the potential mechanisms driving long‐term climate induced change. In particular, we find that birds are affected by winter, spring, and summer conditions depending on the distinct breeding phenology that corresponds to their migratory strategy. Birds in general benefit from higher temperatures or higher primary productivity early on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach will be of general use when high‐resolution time series are available in large‐scale biodiversity surveys.     

Spatial variation in adult sex ratio across multiple scales in the invasive golden apple snail,Pomacea canaliculata

Adult sex ratio (ASR) has critical effects on behavior and life history and has implications for population demography, including the invasiveness of introduced species. ASR exhibits immense variation in nature, yet the scale dependence of this variation is rarely analyzed. In this study, using the generalized multilevel models, we investigated the variation in ASR across multiple nested spatial scales and analyzed the underlying causes for an invasive species, the golden apple snail Pomacea canaliculata. We partitioned the variance in ASR to describe the variations at different scales and then included the explanatory variables at the individual and group levels to analyze the potential causes driving the variation in ASR. We firstly determined there is a significant female‐biased ASR for this species when accounting for the spatial and temporal autocorrelations of sampling. We found that, counter to nearly equal distributed variation at plot, habitat and region levels, ASR showed little variation at the town level. Temperature and precipitation at the region level were significantly positively associated with ASR, whereas the individual weight, the density characteristic, and sampling time were not significant factors influencing ASR. Our study suggests that offspring sex ratio of this species may shape the general pattern of ASR in the population level while the environmental variables at the region level translate the unbiased offspring sex ratio to the female‐biased ASR. Future research should consider the implications of climate warming on the female‐biased ASR of this invasive species and thus on invasion pattern.     

COMPARATIVE CYTOLOGY AND TAXONOMY OF THE ULVAPHYCEAE. I. THE ZOOSPORE OF ULOTHRIX ZONATA (CHLOROPHYTA)1

This fine structural study of the quadriflagellate zoospore of Ulothrix zonata (Weber & Mohr) Kützing, with special attention to the flagellar root system, demonstrates that it is very similar to the zoospore of Ulva lactuca L. in several aspects. Common features include the presence of a cruciate root system (4-2-4-2 type), a non-striated band that connects basal bodies, a so-called terminal cap, and system I and system II striated root components. Only slight differences exist, i.e. in the shape of the terminal cap, and in the number and position of the system II root components. It is concluded that the taxonomic affinities of U. zonata lie with the Ulvaphyceae sensu Stewart and Mattox rather than with the Chlorophyceae. Additional support for this conclusion is the discovery of tiny, flat body scales on the zoospore of U. zonata. A summary of the distinctive characteristics of the Chlorophyceae, Charophyceae and Ulvaphyceae reflecting the current state of knowledge is given.