Proteins are vital biological macromolecules that execute biological functions and form the core of synthetic biological systems. The history of de novo protein has evolved from initial successes in subordinate structural design to more intricate protein creation, challenging the complexities of natural proteins. Recent strides in protein design have leveraged computational methods to craft proteins for functions beyond their natural capabilities. Molecular dynamics (MD) simulations have emerged as a crucial tool for comprehending the structural and dynamic properties of de novo-designed proteins. In this study, we examined the pivotal role of MD simulations in elucidating the sampling methods, force field, water models, stability, and dynamics of de novo-designed proteins, highlighting their potential applications in diverse fields. The synergy between computational modeling and experimental validation continued to play a crucial role in the creation of novel proteins tailored for specific functions and applications.

The origin and development of the Journal of the Marine Biological Association of the United Kingdom is described on the occasion of the publication of the 100th volume. Papers in the Journal demonstrate how the techniques and approaches to the study of the marine environment have evolved over the 120 years of publication. The early papers provided a baseline description of the marine environment and of marine communities that allowed the effects of later perturbations of the environment to be determined. Both the early papers and the long time series of records have proved to be particularly relevant as marine scientists try to predict the long-term results of climatic and anthropogenic effects on the marine ecosystem. The Journal has now become increasingly international, with most papers coming from outside Europe.

The invasive ascidian Ciona intestinalis is irregularly and narrowly distributed in a few areas on the Brazilian coast. It was recorded in the States of Paraná, São Paulo, and Rio de Janeiro. In the State of Rio de Janeiro, all records refer to the Guanabara Bay, a polluted environment that probably hosts other introduced species. Ciona intestinalis was last recorded in this bay in 1991. Given the absence of records since then, researchers concluded that it had been extinct there, and even from the Brazilian coast. During our experiment, conducted with predator exclusion and light attenuation, we collected some samples of C. intestinalis, which suggests that it has either been reintroduced in the Guanabara Bay or that its presence there is a consequence of predator exclusion. Ciona intestinalis was found inside boxes with low luminosity, whose openings were turned to the bottom and protected with a net for predator exclusion. This method was successfully used 17 years ago, when numerous species samples were detected. Our conclusion is that the irregular recording of C. intestinalis on the Brazilian coast, in both time and space, probably derives from inappropriate techniques and methods to sample or observe it on natural substrate. Replicating this methodology in other regions of Brazil and in other South American countries, especially in port areas, would show that the distribution of C. intestinalis is possibly broader than previously reported.

The purpose of the present article is to compare different phase-spacesampling methods, such as purely stochastic methods (Rejection method, Metropolized independence sampler, Importance Sampling),stochastically perturbed Molecular Dynamics methods (Hybrid Monte Carlo, Langevin Dynamics, Biased Random Walk), and purelydeterministic methods (Nosé-Hoover chains, Nosé-Poincaré and RecursiveMultiple Thermostats (RMT) methods). After recalling some theoretical convergence properties forthe various methods, we provide some new convergence resultsfor the Hybrid Monte Carlo scheme, requiring weaker (and easier tocheck) conditions than previously known conditions. We then turn to the numericalefficiency of the sampling schemes for a benchmark model of linearalkane molecules. In particular, the numerical distributions that are generated are compared in a systematic way, on the basisof some quantitative convergence indicators.

One of the most frequently used sampling methods used in defining fish microhabitat is the Point Abundance Sampling byElectrofishing (PASE) technique. Nevertheless this method is size-selective and induces escapement behaviour in most fish species.The aim of this study is first to describe a direct visual fish observation method, the Point Abundance Sampling by Scubadiving (PASS), and second, to compare this method with the classical PASE to determine 0+ (i.e. young of the year) roach(Rutilus rutilus,L.) microhabitat in the littoral zone of a mesotrophic lake.The study was undertaken during summer 1998 in lake Pareloup (south-west France). Sampling was performed weekly in tworestricted littoral areas of the lake which presented the same environmental and topographical characteristics aiming to compare0+ roach habitat features obtained using the two sampling techniques (PASE and PASS). The two data matrices obtained (i.e.PASE and PASS) were used to develop microhabitat preference indices for each of the 9 variables as a measurement of habitatuse by the 0+ roach vs. habitat availability.Even though 0+ roach occurrence and abundance were found to be similar with both methods, microhabitat profiles revealeddifferent patterns. A significant microhabitat difference between the two sampling methods was found using the non-parametricstatistical test of Wilcoxon (Z = -4.20, p < 0.01). We can hypothesise that the differences observed between the two samplingdesigns were due to an escapement behaviour of 0+ roach. Unlike PASS, using PASE, fish are located in «shelter habitats» suchas shallow water and dense vegetation. Such behaviour is caused by the environmental disturbance induced by this samplingmethod. The study reveals that PASS appears to be more suitable than PASE for the assessment 0+ fish microhabitat.

In most real-world contexts the sampling effort needed to attain an accurate estimate of total species richness is excessive. Therefore, methods to estimate total species richness from incomplete collections need to be developed and tested. Using real and computer-simulated parasite data sets, the performances of 9 species richness estimation methods were compared. For all data sets, each estimation method was used to calculate the projected species richness at increasing levels of sampling effort. The performance of each method was evaluated by calculating the bias and precision of its estimates against the known total species richness. Performance was evaluated with increasing sampling effort and across different model communities. For the real data sets, the Chao2 and first-order jackknife estimators performed best. For the simulated data sets, the first-order jackknife estimator performed best at low sampling effort but, with increasing sampling effort, the bootstrap estimator outperformed all other estimators. Estimator performance increased with increasing species richness, aggregation level of individuals among samples and overall population size. Overall, the Chao2 and the first-order jackknife estimation methods performed best and should be used to control for the confounding effects of sampling effort in studies of parasite species richness. Potential uses of and practical problems with species richness estimation methods are discussed.

In order to develop suitable sampling methods for the arthropods of four mint species, namely Japanese mint (Mentha arvensis L.- var. Hybrid 77), peppermint (M. piperitaL.-var. MP-1), bergamot mint (M. citrata Ehrhrt- var. Kiran) and spearmint (M. spicata L.- var. MSS-5), six general sampling methods viz. ground cloth, sticker, sweep net, water trap, whole plant observation (WPO) and whole plant harvest (WPH) were evaluated under field conditions at the Research Farm of Central Institute of Medicinal and Aromatic Plants, Lucknow, India. The mint pest complex on all the mint species included Aphis craccivora, Chrotogonus trachypterus, Leptocorisa varicornis, Coccinella septempunctata, Bemisia tabaci, an unidentified lygeid bug, Brumoides suturalis, Propylea dissecta, Crysolina exanthematica, Dysdercus cingulatus and Plusia orichalcea. Overall, the ground cloth, sweep net, water trap and sticker methods were found to be more efficient and successful for sampling the arthropods of mint crops than the WPO and WPH methods. The shortest sampling time was required when using the sticker (3–6 seconds per sweep) and the sweep net (7–8 seconds per sweep) methods. This information may be useful in developing an integrated pest management programme for mint.

Observation on the distribution and seasonal variation of riverine tsetse population at Egbe in the Derived Savanna Zone of Nigeria was made and compared with variation in other vegetation types of the country. Egbe, in a sub-humid location, was observed to have a low rainy/high dry season population density similar to what occurs in part of the Southern Guinea Savanna Zone. To the north of these areas, the less humid vegetation zones show a definite reverse pattern (high rainy/low dry season) of seasonal population density. The Rain Forest Belt, a humid zone has, surprisingly, more similarity with the less humid zones to its far north than with the sub-humid zones nearer to it Irrespective of zone and season, a favourable temperature of between 26.1 and 26.7°C appeared important towards having a high population density. Reasons were given for the low rainy season tsetse density at Egbe. Unlike zones in the less humid north where rainy season dispersal is well marked, tsetse distribution in the Derived Savanna Zone remained by the riverine vegetation almost throughout the year. The advantage of this study to a proposed ranch for the area was highlighted.

A year round ecological study of Glossina morsitans submorsitans variety ugandensis was carried out from September 1980 to August 1981 in the Finchaa river valley in the western part of Ethiopia. Two sampling methods, namely vehicle patrol and screen/handnet capture were employed. The latter was more efficient. The effect of various environmental factors (e.g. altitude, climate, vegetation etc.) that determine the eco-distribution of this species of tsetse were analysed. The most significant finding was that tsetse were distributed far above the previously known altitude limits.

A study was carried out during the wet and dry seasons, between October 1978 and May 1980 (altogether comprising four wet and three dry seasons), on the trypanosome infection rate in the tsetse species, Glossina pallidipes Austen, in rural situations in the Kiboko and Nkruman areas in Kenya. There were some sex and age differences with respect to trypanosome infection. Female tsetse showed higher infection rates, and old flies, both male and female, also showed relatively higher trypanosome infection rates. Infections with Trypanosoma vivax and T. congolense were different, both as regards to seasons and locality: the infection rate with the latter was higher in Kiboko than in Nkruman, and varied seasonally; while the infection rate with T. vivax did not vary significantly with seasons. The kind of traps used for sampling tsetse influenced the trypanosome infection rate indirectly by having a direct influence on the age structure of tsetse. The vertebrate hosts of tsetse in the two areas played an important role: the infection rates of tsetse with T. vivax and T. congolense were high in areas with a high density of bovids.