The Aragonian and Vallesian high-resolution micromammal succession from the Calatayud-Montalbán Basin (Aragón,Spain)

We present an updated taxonomy and faunal distribution of the micromammal fossil record from the Aragonian and Lower Vallesian of the Calatayud-Montalbán Basin. The analysed record includes the orders Rodentia, Eulipotyphla, and Lagomorpha. The pattern of species turnover shows seven major faunal events, which are correlated with major climate changes based on marine stable oxygen and carbon isotope records. Episodes δ¹⁸O Mi-2 and Mi-3 are significantly correlated with major micromammal turnover at the boundaries between the Lower and Middle Aragonian and the Middle and Upper Aragonian, respectively. Our results support the existence of a selective turnover during the Aragonian and Lower Vallesian.     

The role of screening and treatment in the transmission dynamics of HIV/AIDS and tuberculosis co-infection: a mathematical study

In this paper, we present a deterministic non-linear mathematical model for the transmission dynamics of HIV and TB co-infection and analyze it in the presence of screening and treatment. The equilibria of the model are computed and stability of these equilibria is discussed. The basic reproduction numbers corresponding to both HIV and TB are found and we show that the disease-free equilibrium is stable only when the basic reproduction numbers for both the diseases are less than one. When both the reproduction numbers are greater than one, the co-infection equilibrium point may exist. The co-infection equilibrium is found to be locally stable whenever it exists. The TB-only and HIV-only equilibria are locally asymptotically stable under some restriction on parameters. We present numerical simulation results to support the analytical findings. We observe that screening with proper counseling of HIV infectives results in a significant reduction of the number of individuals progressing to HIV. Additionally, the screening of TB reduces the infection prevalence of TB disease. The results reported in this paper clearly indicate that proper screening and counseling can check the spread of HIV and TB diseases and effective control strategies can be formulated around ‘screening with proper counseling’.     

Dynamic simulation of pollutant effects on the threonine pathway in Escherichia coli

The enzymatic activities of threonine pathway in Escherichia coli are sensitive to pollutants such as cadmium, copper and mercury, which, even at low concentration, can substantially decrease or even block the pathway at several steps. Our aim was to investigate the complex effects on a metabolic pathway of such general enzyme inhibitors with several sites of action, using a previously developed computer simulation of the pathway. For this purpose, the inhibition parameters were experimentally determined and incorporated in the model. The calculation of the flux control coefficient distribution between the five steps of the threonine pathway showed that control remains shared between the three first steps under most inhibition conditions. Response coefficient analysis shows that the inhibition of aspartate semialdehyde dehydrogenase is quantitatively dominant in most circumstances.     

Dehydrogenases reducing NAD+ in the presence of D (-) 3- phosphoglycerate in mycobacteria (BCG, H37Ra, M. phlei)]

Referring to the elution volume on a Sephadex G-150 column only one specific peak is obtained, the same for the BCG, H37Ra and Mycobacterium phlei strains grown on Sauton synthetic medium. Some properties of these partially purified dehydrogenases are studied (conservation and dialysis in media of different salt concentrations, equilibrium constant, Km, heat stability). All enzyme preparations from tubercle bacilli (BCG, H37Ra) are readily inactivated by heat and are very unstable in solutions of low ionic strength. In contrast, under the same experimental conditions, all enzyme samples from M. phlei are, comparatively, much more stable towards these factors [heat, salt (potassium phosphate, NaCl) concentration].     

Probing the combination of erlotinib hydrochloride,an anticancer drug,and human serum albumin: Spectroscopic,molecular docking,and molecular dynamic analyses

Human serum albumin (HSA) is a globular and monomeric protein in plasma that transports many drugs and compounds. Binding of some drugs to HSA can lead to changes in its stability and biological function. We investigated the binding interactions between erlotinib hydrochloride (Erlo) and HSA. Erlo is used to treat lung, pancreatic, and some other cancers. Experimental data showed that the fluorescence emission of the protein was quenched by Erlo using a static quenching mechanism. The calculation of the binding constant, K_b (1.57 × 10⁵ M⁻¹ at 300 K), confirmed the existence of a moderate binding interaction between Erlo and HSA. The interaction was enthalpy driven, spontaneous, and exothermic. The calculated thermodynamic parameters in agreement with simulation and molecular docking data showed that van der Waals and hydrogen bond forces played an important role in the interaction process. Molecular docking results indicated that Erlo has more affinity to bind to subdomain IIA (site I) of HSA. Molecular dynamics simulation analysis showed that the protein is stable in the presence of Erlo under simulation conditions.     

Reproductive phenology of a natural population of Armadillidium pelagicum Arcangeli, 1955 (Isopoda, Oniscidea)

Armadillidium pelagicum, the most abundant species of the genus in Tunisia is endemic to the North of Tunisia and the circumsicilian islands. In the laboratory and under the natural conditions of temperature and photoperiod, virgin females of A. pelagicum exhibit a spontaneous ovarian maturation, followed by a parturial moult. Nevertheless, the onset of reproduction is greatly accelerated by the presence of a male. In fact, mating shortened the lag time (from the beginning of experiment to the parturial moult) by reducing the number of normal moult preceding the first parturial moult and the duration of the preparturial intermoult. In this species, only one mating is enough to ensure the fertility for several egg layings. Otherwise, it has been shown that A. pelagicum has a reproductive period rather than a reproductive activity and that mating females have a longer reproductive period than virgins. Like several species of terrestrial Isopods, the duration of the gestation period is temperature-dependent.     

Analysis of fragments induced by simulated lattice protein folding

The folding process of a set of 42 proteins, representative of the various folds, has been simulated by means of a Monte Carlo method on a discrete lattice, using two different potentials of mean force. Multiple compact fragments of contiguous residues are formed in the simulation, stable in composition, but not in geometry. During time, the number of fragments decreases until one final compact globular state is reached. We focused on the early steps of the folding in order to evidence the maximum number of fragments, provided they are sufficiently stable in sequence. A correlation has been established between these proto fragments and regular secondary-structure elements, whatever their nature, alpha helices or beta strands. Quantitatively, this is revealed by an overall mean one-residue quality factor of nearly 60%, which is better for proteins mainly composed of alpha helices. The correspondence between the number of fragments and the number of secondary-structure elements is of 77% and the regions separating successive fragments are mainly located in loops. Besides, hydrophobic clusters deduced from HCA correspond to fragments with an equivalent accuracy. These results suggest that folding pathways do not contain structurally static intermediate. However, since the beginning of folding, most residues that will later form one given secondary structure are kept close in space by being involved in the same fragment. This aggregation may be a way to accelerate the formation of the native state and enforces the key role played by hydrophobic residues in the formation of the fragments, thus in the folding process itself.     

Climatic and environmental conditions from the Neolithic to the Bronze Age (7000–3000 BP) in the Iberian Peninsula assessed using small-mammal assemblages

We have analyzed the palaeoenvironment and palaeoclimate of the beginning of the Holocene in the Iberian Peninsula on the basis of the small-mammal assemblages from three sites within the geography of the Iberian Peninsula: Mirador (Sierra de Atapuerca, Burgos), Colomera (Sant Esteve de la Sarga, Lleida) and Valdavara-1 (Becerreá, Lugo). These associations reveal that the palaeoenvironment was more humid than today in the sites under study, and the landscape was dominated by woodland and woodland margins in all the studied layers. Further, the climatic conditions were stable, but with winters colder than at present, above all in the Mediterranean area. Finally, our data have been compared with other environmental and climatic proxies, showing that human activities exerted little impact on the palaeoenvironmental conditions that occurred from 7000 to 3000 BP in the Iberian Peninsula.     

Effect of including genetic progress in milk yield on evaluating the use of sexed semen and other reproduction strategies in a dairy herd

The objective of this study was to explore the importance of including genetic progress in milk yield when evaluating different reproductive strategies in a dairy herd by simulation modeling. The model used in this study was SimHerd V, a dynamic and mechanistic Monte Carlo simulation model of a dairy herd including young stock. A daily increasing trend describing genetic milk yield potential of the sire population was included in the model. The inaccuracy of assuming that replacement heifers have the same (milk yield) potential as the cows present in the herd was hereby dealt with. Improving estrus detection rate from 0.45 to 0.80 increased gross margin (GM) per cow-year by €20 when genetic progress was not included in the model. When genetic progress was included in the model, then the same improvement in estrus detection decreased the GM per cow-year by €7.4. This reduced effect was explained by a lower replacement rate in consequence of the improved estrus detection and thereby a slower genetic progress in the herd. There was a reduced effect of including genetic progress on GM when surplus heifers were sold selectively based on breeding values. Repeated insemination with sexed semen on the superior half of all heifers reduced GM by €8 per cow-year when genetic progress was not included and increased the GM by €16 per cow-year when genetic progress was included in the model. Including genetic progress reduced the losses caused by lower conception and estrus detection rates and had a minimal effect with regard to postponing first insemination. This study has proven that it is important to include genetic progress in decisions on reproduction strategies in a dairy herd.     

Mathematical approaches to differentiation and gene regulation

We consider some mathematical issues raised by the modelling of gene networks. The expression of genes is governed by a complex set of regulations, which is often described symbolically by interaction graphs. These are finite oriented graphs where vertices are the genes involved in the biological system of interest and arrows describe their interactions: a positive (resp. negative) arrow from a gene to another represents an activation (resp. inhibition) of the expression of the latter gene by some product of the former. Once such an interaction graph has been established, there remains the difficult task to decide which dynamical properties of the gene network can be inferred from it, in the absence of precise quantitative data about their regulation. There mathematical tools, among others, can be of some help. In this paper we discuss a rule proposed by Thomas according to which the possibility for the network to have several stationary states implies the existence of a positive circuit in the corresponding interaction graph. We prove that, when properly formulated in rigorous terms, this rule becomes a theorem valid for several different types of formal models of gene networks. This result is already known for models of differential [C. Soulé, Graphic requirements for multistationarity, ComPlexUs 1 (2003) 123-133] or Boolean [E. Rémy, P. Ruet, D. Thieffry, Graphic requirements for multistability and attractive cycles in a boolean dynamical framework, 2005, Preprint] type. We show here that a stronger version of it holds in the differential setup when the decay of protein concentrations is taken into account. This allows us to verify also the validity of Thomas' rule in the context of piecewise-linear models. We then discuss open problems.     

Continental gateways and the dynamics of mammalian faunas

Continental gateways occur where mountainous topography interacts with changing climate and sea level to open or close dispersal corridors. The interaction of permeable or impermeable montane barriers with changing or stable climate yields four biogeographic states, each associated with changes in diversification rates and ecological structure of faunas. For example, permeable montane barriers and climatic stability result in low rates of immigration and extinction, elevated endemic speciation, and stable ecological structure. Three examples from the mammalian fossil record test these scenarios. (1) In Miocene faunas of Pakistan, immigration rates peaked and faunal proportions changed during an interval of cooling and open corridors. (2) In Miocene faunas of Spain, elevated extinction and origination rates and changing trophic structure occurred during regional aridification with open corridors. (3) In Quaternary faunas of South Africa, ungulates experienced range reductions and elevated extinction during the transition from glacial to interglacial climates as corridors closed.     

A new Late Pleistocene non-anthropogenic vertebrate assemblage from the northern Iberian Peninsula: Artazu VII (Arrasate,Basque Country)

Late Pleistocene palaeontological sites without human intervention are limited in the Cantabrian region, and even more so those with a good state of preservation and rich biodiversity. A new vertebrate fossiliferous locality discovered at Kobate Quarry (Arrasate, northern Iberian Peninsula) is presented in this article. This site, in which remains of 40 different vertebrate taxa were accumulated, acted as a natural trap. The preliminary vertebrate faunal list includes five amphibian taxa, four reptiles, seven species of birds and 24 mammalian taxa. While small mammals are represented by 13 small mammal taxa (seven in the Order Rodentia, five in the Order Eulipotyphla, and one in the Order Chiroptera), the large mammal fauna comprises eleven species, including ungulates and carnivores. The palaeoecology inferred from this faunal assemblage suggests the existence of large forested areas with some grassland and a watercourse nearby, within a notably warm and humid climate. These palaeoenvironmental conditions, combined with AMS and AAR results carried out in macrofaunal bone samples, suggest that the deposit from Artazu VII would be located in the first half of the Late Pleistocene, in the Marine Isotope Stage (MIS) 5c.     

Recent aspects of genetic manipulation in Bacillus thuringiensis

The conjugative plasmid pAM beta 1 was transferred from Streptococcus faecalis to several strains of Bacillus thuringiensis by a filter-mating process. From a transconjugant clone of B. thuringiensis a hybrid plasmid resulting from an in vivo insertion into pAM beta 1 of a 3 Md DNA sequence was isolated. This 3 Md DNA molecule (Th sequence) is related to several host plasmids found in different serotypes of B. thuringiensis. A reciprocal conjugation-like process involving the transfer of pAM beta 1 from B. thuringiensis to S. faecalis was also demonstrated. The comparison of the restriction maps of the crystal genes from plasmid and chromosomal origins of different serotypes, six of which having been cloned in E. coli, revealed the existence of two classes of genes which are very similar in the map corresponding to the N-terminal part of the protein, and which differ essentially in the 3' region. The presence of the transposon-like Th sequence was found in several cases associated with the crystal gene in the same host plasmid, and a model for their structural organization is proposed.     

Woody macroremains from the Acheulian site of Torralba: Occurrence and palaeoecology of Pinus cf. sylvestris in the Middle Pleistocene of the Iberian Peninsula

The pieces of wood extracted by the Marquis of Cerralbo at the Acheulian site of Torralba constitute one of the few materials from this famous locality that have not been subjected to detailed study by researchers. Over a century after their extraction, the present paper provides the first anatomical results of these 34 woody remains. The results highlight the presence of the taxon Pinus sylvestris–nigra group (Pinus cf. sylvestris) at the site, thus constituting one of the few and oldest references attributable to the aforementioned taxon for the Iberian Peninsula. The anatomical diagnosis confirms the existence of Middle Pleistocene landscapes with pine woods at elevations at least 200 m lower than at present in the site area. From a taphonomic point of view, the wood samples exhibit the typical morphologies of woody macroremains preserved in continental sedimentary environments, and there was no evidence at all that they had previously been manipulated by man.     

The transmission dynamic of different hepatitis B-infected individuals with the effect of hospitalization

We propose an epidemic model for the transmission of hepatitis B virus along with the classification of different infection phases and hospitalized class. We formulate the model and discuss its basic mathematical properties, e.g. existence, positivity, and biological feasibility. Exploiting the next generation matrix approach, we find the basic reproductive number of the model. We perform sensitivity analysis to illustrate the effect of various parameters on the transmission of the disease. We investigate stability of the equilibria of the model in terms of the basic reproduction number. Conditions for the stability of the proposed model are obtained using various approaches. Finally, we perform the numerical simulations to discuss sensitivity analysis and to support our analytical work.     

具有周期传染率的SIR传染病模型的周期解

考虑了具有周期传染率的SIR流行病模型,定义了基本再生数^-R0=β／（μ＋γ）,分析了该模型的动力学性态,证明了当^-R0〈1时无病平衡点是全局稳定的;^-R0〉1时,无病平衡点是不稳定的,模型至少存在一个周期解。对小振幅的周期传染率模型,给出了模型周期解的近似表达式,证明了该周期解的稳定性,最后做了数值模拟,结果显示周期解可能是全局稳定的。     

A study of the Coriolis effect on the fluid flow profile in a centrifugal bioreactor

Increasing demand for tissues, proteins, and antibodies derived from cell culture is necessitating the development and implementation of high cell density bioreactors. A system for studying high density culture is the centrifugal bioreactor (CCBR), which retains cells by increasing settling velocities through system rotation, thereby eliminating diffusional limitations associated with mechanical cell retention devices. This article focuses on the fluid mechanics of the CCBR system by considering Coriolis effects. Such considerations for centrifugal bioprocessing have heretofore been ignored; therefore, a simpler analysis of an empty chamber will be performed. Comparisons are made between numerical simulations and bromophenol blue dye injection experiments. For the non‐rotating bioreactor with an inlet velocity of 4.3 cm/s, both the numerical and experimental results show the formation of a teardrop shaped plume of dye following streamlines through the reactor. However, as the reactor is rotated, the simulation predicts the development of vortices and a flow profile dominated by Coriolis forces resulting in the majority of flow up the leading wall of the reactor as dye initially enters the chamber, results are confirmed by experimental observations. As the reactor continues to fill with dye, the simulation predicts dye movement up both walls while experimental observations show the reactor fills with dye from the exit to the inlet. Differences between the simulation and experimental observations can be explained by excessive diffusion required for simulation convergence, and a slight density difference between dyed and un‐dyed solutions. Implications of the results on practical bioreactor use are also discussed. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

A tunable multivariable nonlinear robust observer for biological systems

This paper presents a robust nonlinear asymptotic observer with adjustable convergence rate with a great potential of applicability for biological systems in which the main state variables are difficult and expensive to measure or such measurements do not exist. This observer scheme is based on the classical asymptotic observer, which is modified to allow the tuning of the convergence rate. It is shown that the proposed observer provides fast and satisfactory estimates when facing load disturbances, system failures and parameter uncertainty while maintaining the excellent robustness and stability properties of the classical asymptotic observer. The implementation of the tunable observer is carried out by numerical simulations of a mathematical model of an anaerobic digestion process used for wastewater treatment. The key results are examined and further developed.     

Mathematical modeling and qualitative analysis of insulin therapies

Several insulin therapies are widely in clinical use with the basic strategy that mimics insulin secretion in a normal glucose-insulin endocrine metabolic regulatory system. In this paper, we model the insulin therapies using a delay differential equation model. We study the dynamics of the model both qualitatively and quantitatively. The analytical results show the existence and uniqueness of a stable periodic solution that corresponds to ultradian insulin secretion oscillations. Numerically we simulate the insulin administration based on our model. The numerical simulation results are in agreement with findings of clinical studies.     

Mathematical model of proliferative activity in epidermis of the normal skin and of the skin afflicted by psoriasis

A mathematical model of the mitotic activity of epidermis in norm and psoriasis is presented, which consists of a system of two autonomous nonlinear differential equations. A qualitative analysis of the model was done, and numerical solutions at the parameter values corresponding to these state were obtained. It was shown that, in norm, the system can exist only in one stationary equilibrium state of the "focus" type, and in psoriasis, due to an increase in the growing fraction, hyperproliferation, and enhanced migration of keratinocytes, a stable limiting cycle arises from the state of an unstable focus. The existence of two stable states (focus and the limiting cycle) is regulated by a parameter that describes the inhibition of division of maturing cells of suprabasal epidermal layers by the intrinsic tissue-specific transmitters of mitosis of G1-keilon type. The model is consistent with experimental data on the kinetics of cell proliferation in the epidermis in norm and psoriasis and the clinical course of the disease.