Factors influencing natural fecundity in fertile couples: a survey of puerperae and their partners.

RESEARCH QUESTION: What is the fecundity rate among fertile couples, and which factors influence it? DESIGN: Retrospective study of all puerperae attending Cruces University Hospital Human Reproduction Unit over 9 months. An anonymous questionnaire was circulated to all patients, and 2510 valid completed questionnaires were collected. The main inclusion criterion was natural conception resulting in delivery. Pregnancies resulting from ART and contraceptive method failure were excluded. Investigated parameters were time to pregnancy, age and smoking (in women and men), previous pregnancies and intercourse frequency. A mathematical formula was developed to predict the per-month fecundity rate (PMFR). RESULTS: The cumulative fecundity rate was 29.08%, 54.26%, 68.61%, 89.88%, 96.95% and 98.63% (at 1, 3, 6, 12, 24 and 36 months); between 12 and 36 months, the average PMFR ranged from 8.53-7.48%. Only 1.68% of pregnancies occurred between 24 and 36 months, and only 1.37% thereafter. The best fecundity markers were obtained in the group who had sexual intercourse seven to eight times a week. Women and men younger than 25 years had lower fecundity markers than those aged between 25 and 40 years. CONCLUSIONS: Fertile couples have a non-negligible per-month fecundity rate between 12 and 36 months, which should be considered when planning fertility studies. The lower fecundity rate observed in women and men aged younger than 25 years deserves more study. Coital frequencies of more than two or three times a week did not affect the fecundity rate and was better with frequencies of seven to eight times a week.

Lessons learned from 64,071 embryos subjected to PGT for aneuploidies: results, recurrence pattern and indications analysis.

RESEARCH QUESTION: What is the influence of biological, technical and clinical factors on embryo outcomes in preimplantation genetic testing for aneuploidies (PGT-A) and what is the recurrence pattern? DESIGN: This retrospective study included 64,071 embryos undergoing PGT-A in the same laboratory between 2011 and 2019. Biopsies were performed at the day 3 embryo stage (48.32%) or blastocyst stage (51.70%). Advanced maternal age (AMA) was the main indication (65.62%). RESULTS: The aneuploidy rate was 67.75%, higher in women aged over 35 years than in women aged 35 years or less (71.76% versus 47.44%), and higher in day 3 embryo versus blastocyst biopsies (77.51% versus 58.62%). The trisomy:monosomy ratio was 1.01 for blastocysts versus 0.84 for day 3 embryos. Trisomy 21 was present in 4.9% of embryos. In aneuploid embryos, the probability of having one or more involved chromosomes followed a decreasing exponential pattern. The probability of an embryo being euploid was constant at around 30% (40% in blastocysts, 20% in day 3 embryos). The cumulative probability of having one or more euploid embryos after 10 biopsied embryos was 94.79% in blastocysts and 80.61% in day 3 embryos. AMA was associated with a much higher aneuploidy rate than all other indications, which among them had similar aneuploidy rate and chromosomal involvement. CONCLUSIONS: There is a considerably lower aneuploidy rate in blastocysts than day 3 embryos, which is most notable for monosomies. While AMA shows an increased aneuploidy rate and a specific chromosomal pattern of involvement, the remaining indications showed a similar aneuploidy rate and chromosomal pattern. Even after producing many consecutive aneuploid embryos, the possibility of obtaining a euploid embryo is not negligible.

Computational and Experimental Evaluation of the Immune Response of Neoantigens for Personalized Vaccine Design.

In the last few years, the importance of neoantigens in the development of personalized antitumor vaccines has increased remarkably. In order to study whether bioinformatic tools are effective in detecting neoantigens that generate an immune response, DNA samples from patients with cutaneous melanoma in different stages were obtained, resulting in a total of 6048 potential neoantigens gathered. Thereafter, the immunological responses generated by some of those neoantigens ex vivo were tested, using a vaccine designed by a new optimization approach and encapsulated in nanoparticles. Our bioinformatic analysis indicated that no differences were found between the number of neoantigens and that of non-mutated sequences detected as potential binders by IEDB tools. However, those tools were able to highlight neoantigens over non-mutated peptides in HLA-II recognition (p-value 0.03). However, neither HLA-I binding affinity (p-value 0.08) nor Class I immunogenicity values (p-value 0.96) indicated significant differences for the latter parameters. Subsequently, the new vaccine, using aggregative functions and combinatorial optimization, was designed. The six best neoantigens were selected and formulated into two nanoparticles, with which the immune response ex vivo was evaluated, demonstrating a specific activation of the immune response. This study reinforces the use of bioinformatic tools in vaccine development, as their usefulness is proven both in silico and ex vivo.

Physical activity and sperm quality: influence in sperm donors.

PURPOSE: To ascertain whether physical activity (PA) is associated with better sperm quality in sperm donors. METHODS: A prospective case-control study was designed in an IVF center setting. A total of 207 sperm donation candidates from a relatively small geographical area were included in the study with no intervention. Donor candidates were subjected to conventional sperm analysis according to WHO criteria. Moreover, they answered a standardized questionnaire regarding their last week PA (IPAQ), with PA expressed in metabolic equivalents (METs)-min/week. Donors were classified into 4 groups: low, moderate, high and very high PA. Specific sports were included in the questionnaire. Semen samples from 43 accepted donors were used in artificial insemination by donor (AID) and IVF. The fertilization rates (FR) and pregnancy rates (PR) were studied. RESULTS: Semen volume, sperm concentration, progressive spermatozoa, non-progressive spermatozoa, total motile progressive spermatozoa and sperm morphology were similar in the four PA groups. No correlation between various semen parameters studied and METs was found. Running or cycling > 1 h/week did not influence sperm parameters. The AID PR was similar in the different PA groups. However, in IVF the mean donor FR was significantly higher in the high PA group and in the very high PA group. CONCLUSIONS: No detrimental effect was associated with PA, or even very high PA, regarding conventional sperm parameters. Moreover, a better FR was associated with high and very high PA in IVF cycles, which merits more studies.

Meta-analysis of the embryo freezing transfer interval.

BACKGROUND: The decision of whether frozen embryo transfer (FET) should be performed in the cycle immediately after OPU or at least one cycle later is controversial. FET could improve pregnancy rates in IVF; however, how much time is needed for the endometrium to return to optimal receptivity after ovarian stimulation is not known. METHODS: Electronic search in MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials to identify studies providing data on the influence of the interval between embryo freezing (or OPU) and FET in FET cycles published between January 1, 2007, and February 1, 2020. MAIN FINDINGS: Data analyzed indicated that in the immediate FET cycles, there was a trend to an increased biochemical pregnancy rate (RR = 1.08; CI = 1.00-1.18), whereas the clinical pregnancy rate was somewhat higher, but without reaching statistical significance (RR = 1.07; CI = 0.99-1.15). The live birth rate was similar in the two groups (RR = 1.05; CI = 0.95-1.15), as was the implantation rate (RR = 0.98; CI = 0.83-1.16). Stratifying by embryo stage or FET type (freeze-all or FET after failed fresh transfer) showed no differences. CONCLUSION: Systematically delaying FET does not offer benefits to IVF outcomes. In addition, immediate transfer is associated with a nonsignificant trend to better clinical pregnancy rate and it also avoids the psychological effects of prolonging the stress on prospective parents.

Cervical pregnancy in assisted reproduction: an analysis of risk factors in 91,067 ongoing pregnancies.

RESEARCH QUESTION: What is the frequency of cervical pregnancy in women undergoing assisted reproductive technologies (ART) and what are the risk factors? DESIGN: Case-control study of women undergoing assisted reproductive technology (ART) at 25 private assisted reproduction clinics run by the same group in Spain. Two control groups (tubal ectopic pregnancies and intrauterine pregnancies) were established. The main outcome measure was frequency of cervical pregnancy. Demographic, clinical factors and IVF parameters were assessed for their influence on cervical pregnancy risk. RESULTS: Thirty-two clinical pregnancies were achieved out of 91,067 ongoing pregnancies, yielding a rate of 3.5/10,000. Cervical pregnancies represented 2.02% of all ectopic pregnancies (32/1582). The main risk factors two or more previous pregnancies (OR 2.68; CI 1.18 to 6.07); two or more previous miscarriages (OR 4.21; CI1.7 to 10.43), one or more previous curettages (OR 3.99, CI 1.67 to 9.56), two or more previous curettages (OR 4.71; CI 1.19 to 18.66) and smoking (OR 2.82 CI 1.14 to 6.94). History of caesarean sections and tubal pregnancy was not associated with an elevated cervical pregnancy risk. Infertility conditions and endometrial thickness were similar across the three groups. The proportion of women from whom fewer than 10 oocytes were retrieved was higher in the clinical pregnancy group than in the IUP group. CONCLUSIONS: In ART, the main risk factors for cervical ectopic pregnancy are a history of at least two pregnancies, miscarriages, at least one curettage and smoking. IVF parameters do not seem to influence the development of clinical pregnancies. Cervical pregnancies are less common in ART than previously reported, attributable to improvements in ART; a publication bias in early IVF reports cannot be ruled out.

Labor estimation by informational objective assessment (LEIOA) for preterm delivery prediction.

PURPOSE: To introduce LEIOA, a new screening method to forecast which patients admitted to the hospital because of suspected threatened premature delivery will give birth in < 7 days, so that it can be used to assist in the prognosis and treatment jointly with other clinical tools. METHODS: From 2010 to 2013, 286 tocographies from women with gestational ages comprehended between 24 and 37 weeks were collected and studied. Then, we developed a new predictive model based on uterine contractions which combine the Generalized Hurst Exponent and the Approximate Entropy by logistic regression (LEIOA model). We compared it with a model using exclusively obstetric variables, and afterwards, we joined both to evaluate the gain. Finally, a cross validation was performed. RESULTS: The combination of LEIOA with the medical model resulted in an increase (in average) of predictive values of 12% with respect to the medical model alone, giving a sensitivity of 0.937, a specificity of 0.747, a positive predictive value of 0.907 and a negative predictive value of 0.819. Besides, adding LEIOA reduced the percentage of incorrectly classified cases by the medical model by almost 50%. CONCLUSIONS: Due to the significant increase in predictive parameters and the reduction of incorrectly classified cases when LEIOA was combined with the medical variables, we conclude that it could be a very useful tool to improve the estimation of the immediacy of preterm delivery.

A combinatorial approach to the design of vaccines.

We present two new problems of combinatorial optimization and discuss their applications to the computational design of vaccines. In the shortest λ-superstring problem, given a family S1,...,S(k) of strings over a finite alphabet, a set Τ of "target" strings over that alphabet, and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ target strings as substrings of S(i). In the shortest λ-cover superstring problem, given a collection X1,...,X(n) of finite sets of strings over a finite alphabet and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ elements of X(i) as substrings. The two problems are polynomially equivalent, and the shortest λ-cover superstring problem is a common generalization of two well known combinatorial optimization problems, the shortest common superstring problem and the set cover problem. We present two approaches to obtain exact or approximate solutions to the shortest λ-superstring and λ-cover superstring problems: one based on integer programming, and a hill-climbing algorithm. An application is given to the computational design of vaccines and the algorithms are applied to experimental data taken from patients infected by H5N1 and HIV-1.

Systemic cellular migration: The forces driving the directed locomotion movement of cells.

Directional motility is an essential property of cells. Despite its enormous relevance in many fundamental physiological and pathological processes, how cells control their locomotion movements remains an unresolved question. Here, we have addressed the systemic processes driving the directed locomotion of cells. Specifically, we have performed an exhaustive study analyzing the trajectories of 700 individual cells belonging to three different species (Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis) in four different scenarios: in absence of stimuli, under an electric field (galvanotaxis), in a chemotactic gradient (chemotaxis), and under simultaneous galvanotactic and chemotactic stimuli. All movements were analyzed using advanced quantitative tools. The results show that the trajectories are mainly characterized by coherent integrative responses that operate at the global cellular scale. These systemic migratory movements depend on the cooperative nonlinear interaction of most, if not all, molecular components of cells.

Endometriosis Increases the Risk of Placenta Previa in Both IVF Pregnancies and the General Obstetric Population.

Is there a relationship between endometriosis and placenta previa (PP)? To investigate if there is a relationship between endometriosis and PP, a retrospective study was carried out, using prospectively recorded data from two different databases from Cruces University Hospital. Two different populations were included in the study. The ART (assisted reproduction techniques) population consisted of 246 cesarean sections (CS), from a total of 1170 deliveries, and the obstetric population consisted of 7045 CS, from a total of 50,298 deliveries. A representative subset from the obstetric population was established selecting 4 CS without PP for each CS with PP. In our ART population, the PP rate was 1.71% among all deliveries and 8.13% among CS. In our general obstetric population, the PP rate was 0.34% among all deliveries and 2.41% among the CS. Among the CS in ART pregnancies, the PP rate was 20% in the women with endometriosis vs 5.47% in women without endometriosis (OR = 4.32; 95% CI = 1.67-11.17), while considering all ART deliveries, the PP rates were 6.43% and 1.07%, respectively (OR = 6.36; 95% CI = 2.59-15.65). In the CS-obstetric population, the rate of PP was 9.61% among women with endometriosis vs 2.19% among women without endometriosis (OR = 4.74; 95% CI = 2.91-7.73). Considering all deliveries, the PP rate was 1.35% among women with endometriosis vs 0.30% in women without endometriosis. Differences persisted when adjusting for age, IVF, multiplicity, and previous deliveries. In the CS-obstetric population with PP, mean surgical time and hospital stay were significantly higher in women with endometriosis. Endometriosis is associated with a higher risk of PP even after adjusting for other parameters.

Comparison of the Administration of 150 or 75 IU of Recombinant LH in Agonist ICSI Cycles Stimulated with Recombinant FSH in Women Aged 35-39: A Comparative Study.

Background: The purpose of the study was to assess whether the coadministration of 150 IU of recombinant LH instead of 75 IU in women aged 35-39 improves the results in agonist ICSI cycles stimulated with 300 IU of recombinant FSH. Methods: In this study, two ovarian stimulation protocols coexisted which were identical except in the administered dose of recombinant LH, for which some patients received 150 IU (n=231) and some received 75 IU (n=216). Both groups received 300 IU of recombinant FSH. Gonadotropins were reimbursed by the National Health System. Statistical analysis was performed by Student's t test, χ2, and ANCOVA. Significance level was established at p=0.05. Results: The number of retrieved oocytes was slightly higher in the 300/150 group (9.06±5.53 vs. 8.61±5.11), but the differences were not significant. Results were similar with the number of metaphase II oocytes (7.18±4.86 vs. 6.72±4.72) and the number of fertilized oocytes (4.64±3.2 vs. 4.23±2.72). The per-transfer clinical pregnancy rates exhibited close similarity between both groups (32.84% vs. 32.46%), as did the per-transfer live birth rates (29.90% vs. 30.37%) and the implantation rate. The rate of hyperstimulation syndrome (OHSS) as well as the rate of cancellation due to OHHS risk was similar in both groups. There was also no difference in the miscarriage rate. When results were expressed by per started cycle or by oocyte pick-up, the results remained very similar in both groups. Conclusion: In women aged 35-39 undergoing ovarian stimulation with recombinant FSH in agonist cycles, the coadministration of 75 or 150 UI of recombinant LH did not influence pregnancy rates. However, a slight increase in the number of retrieved oocytes should not be disregarded.

A Universal Antigen-Ranking Method to Design Personalized Vaccines Targeting Neoantigens against Melanoma.

Background: The main purpose of this article is to introduce a universal mathematics-aided vaccine design method against malignant melanoma based on neoantigens. The universal method can be adapted to the mutanome of each patient so that a specific candidate vaccine can be tailored for the corresponding patient. Methods: We extracted the 1134 most frequent mutations in melanoma, and we associated each of them to a vector with 10 components estimated with different bioinformatics tools, for which we found an aggregated value according to a set of weights, and then we ordered them in decreasing order of the scores. Results: We prepared a universal table of the most frequent mutations in melanoma ordered in decreasing order of viability to be used as candidate vaccines, so that the selection of a set of appropriate peptides for each particular patient can be easily and quickly implemented according to their specific mutanome and transcription profile. Conclusions: We have shown that the techniques that are commonly used for the design of personalized anti-tumor vaccines against malignant melanoma can be adapted for the design of universal rankings of neoantigens that originate personalized vaccines when the mutanome and transcription profile of specific patients is considered, with the consequent savings in time and money, shortening the design and production time.

Testing a vaccine candidate against Hepatitis C virus designed by combinatorial optimization.

This paper presents a new procedure for vaccine design against highly variable viruses such as Hepatitis C. The procedure uses an optimization algorithm to design vaccines that maximize the coverage of epitopes across different virus variants. Weighted epitopes based on the success ratio of immunological assays are used to prioritize the selection of epitopes for vaccine design. The procedure was successfully applied to design DC vaccines loaded with two HCV peptides, STG and DYP, which were shown to be safe, immunogenic, and able to induce significant levels of anti-viral cytokines, peptide-specific cellular immune responses and IgG antibodies. The procedure could potentially be applied to other highly variable viruses that currently lack effective vaccines.

First computational design using lambda-superstrings and in vivo validation of SARS-CoV-2 vaccine.

Coronavirus disease 2019 (COVID-19) is the greatest threat to global health at the present time, and considerable public and private effort is being devoted to fighting this recently emerged disease. Despite the undoubted advances in the development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, uncertainty remains about their future efficacy and the duration of the immunity induced. It is therefore prudent to continue designing and testing vaccines against this pathogen. In this article we computationally designed two candidate vaccines, one monopeptide and one multipeptide, using a technique involving optimizing lambda-superstrings, which was introduced and developed by our research group. We tested the monopeptide vaccine, thus establishing a proof of concept for the validity of the technique. We synthesized a peptide of 22 amino acids in length, corresponding to one of the candidate vaccines, and prepared a dendritic cell (DC) vaccine vector loaded with the 22 amino acids SARS-CoV-2 peptide (positions 50-71) contained in the NTD domain (DC-CoVPSA) of the Spike protein. Next, we tested the immunogenicity, the type of immune response elicited, and the cytokine profile induced by the vaccine, using a non-related bacterial peptide as negative control. Our results indicated that the CoVPSA peptide of the Spike protein elicits noticeable immunogenicity in vivo using a DC vaccine vector and remarkable cellular and humoral immune responses. This DC vaccine vector loaded with the NTD peptide of the Spike protein elicited a predominant Th1-Th17 cytokine profile, indicative of an effective anti-viral response. Finally, we performed a proof of concept experiment in humans that included the following groups: asymptomatic non-active COVID-19 patients, vaccinated volunteers, and control donors that tested negative for SARS-CoV-2. The positive control was the current receptor binding domain epitope of COVID-19 RNA-vaccines. We successfully developed a vaccine candidate technique involving optimizing lambda-superstrings and provided proof of concept in human subjects. We conclude that it is a valid method to decipher the best epitopes of the Spike protein of SARS-CoV-2 to prepare peptide-based vaccines for different vector platforms, including DC vaccines.

Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior.

One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.

Associative Conditioning Is a Robust Systemic Behavior in Unicellular Organisms: An Interspecies Comparison.

The capacity to learn new efficient systemic behavior is a fundamental issue of contemporary biology. We have recently observed, in a preliminary analysis, the emergence of conditioned behavior in some individual amoebae cells. In these experiments, cells were able to acquire new migratory patterns and remember them for long periods of their cellular cycle, forgetting them later on. Here, following a similar conceptual framework of Pavlov's experiments, we have exhaustively studied the migration trajectories of more than 2000 individual cells belonging to three different species: Amoeba proteus, Metamoeba leningradensis, and Amoeba borokensis. Fundamentally, we have analyzed several relevant properties of conditioned cells, such as the intensity of the responses, the directionality persistence, the total distance traveled, the directionality ratio, the average speed, and the persistence times. We have observed that cells belonging to these three species can modify the systemic response to a specific stimulus by associative conditioning. Our main analysis shows that such new behavior is very robust and presents a similar structure of migration patterns in the three species, which was characterized by the presence of conditioning for long periods, remarkable straightness in their trajectories and strong directional persistence. Our experimental and quantitative results, compared with other studies on complex cellular responses in bacteria, protozoa, fungus-like organisms and metazoans that we discus here, allow us to conclude that cellular associative conditioning might be a widespread characteristic of unicellular organisms. This new systemic behavior could be essential to understand some key principles involved in increasing the cellular adaptive fitness to microenvironments.

Effect of vitamin E administered to men in infertile couples on sperm and assisted reproduction outcomes: a double-blind randomized study.

OBJECTIVE: To evaluate the influence on sperm parameters and in vitro fertilization (IVF) outcomes of the administration of 400 mg/day of vitamin E for 3 months to men from infertile couples who are undergoing IVF. DESIGN: Double-blind, placebo-controlled, randomized study. SETTING: Human reproduction unit of a university hospital. PATIENTS: A total of 101 couples, 50 in the vitamin E group and 51 in the placebo group, undergoing IVF, among whom 64.4% of cases had an abnormal spermiogram according to World Health Organization (WHO) criteria. INTERVENTIONS: Vitamin E (α-tocopherol), 400 mg daily by mouth for 3 months, with sperm analysis performed immediately before starting the treatment and 3 months later on the day of IVF. MAIN OUTCOME MEASURES: WHO sperm parameters and IVF outcomes. RESULTS: Although there was a statistically significant increase in progressive motility in the vitamin E group compared with before-treatment values, a similar increase occurred in the placebo group. Normal morphology was even better in the placebo group. Regarding IVF outcomes, better fertilization rates were observed in the placebo group, but the live-birth rate per transfer was statistically significantly higher in the vitamin E group: 17 (41.46%) of 41 versus 9 (20.46%) of 44 in the placebo group. Although the clinical pregnancy rates (both per transfer and per cycle started) and the implantation rate were somewhat higher in the vitamin E group (43.9% and 25%; 36.0% and 22.0%; and 24.7% and 14.1%, respectively), the increase was not statistically significant. CONCLUSIONS: The effect of vitamin E on classic sperm parameters was not an improvement over placebo. Nonetheless, vitamin E administration was associated with a statistically significantly higher live-birth rate, and there was a trend toward better results in other IVF parameters. CLINICAL TRIAL REGISTRATION NUMBER: Eudra CT 2007-000960-25.

Weighted lambda superstrings applied to vaccine design.

We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins.

The nucleus does not significantly affect the migratory trajectories of amoeba in two-dimensional environments.

For a wide range of cells, from bacteria to mammals, locomotion movements are a crucial systemic behavior for cellular life. Despite its importance in a plethora of fundamental physiological processes and human pathologies, how unicellular organisms efficiently regulate their locomotion system is an unresolved question. Here, to understand the dynamic characteristics of the locomotion movements and to quantitatively study the role of the nucleus in the migration of Amoeba proteus we have analyzed the movement trajectories of enucleated and non-enucleated amoebas on flat two-dimensional (2D) surfaces using advanced non-linear physical-mathematical tools and computational methods. Our analysis shows that both non-enucleated and enucleated amoebas display the same kind of dynamic migration structure characterized by highly organized data sequences, super-diffusion, non-trivial long-range positive correlations, persistent dynamics with trend-reinforcing behavior, and move-step fluctuations with scale invariant properties. Our results suggest that the presence of the nucleus does not significantly affect the locomotion of amoeba in 2D environments.

Evidence of conditioned behavior in amoebae.

Associative memory is the main type of learning by which complex organisms endowed with evolved nervous systems respond efficiently to certain environmental stimuli. It has been found in different multicellular species, from cephalopods to humans, but never in individual cells. Here we describe a motility pattern consistent with associative conditioned behavior in the microorganism Amoeba proteus. We use a controlled direct-current electric field as the conditioned stimulus, and a specific chemotactic peptide as the unconditioned stimulus. The amoebae are capable of linking two independent past events, generating persistent locomotion movements that can prevail for 44 min on average. We confirm a similar behavior in a related species, Metamoeba leningradensis. Thus, our results indicate that unicellular organisms can modify their behavior during migration by associative conditioning.