Study of recombinant antibody fragments and PAI-1 complexes combining protein-protein docking and results from site-directed mutagenesis

Elevated plasma levels of plasminogen activator inhibitor-1 (PAI-1) have been correlated with cardiovascular diseases such as myocardial infarction and venous thrombosis. PAI-1 has also been shown to play an important role in tumor development, diabetes, and obesitas. Monoclonal antibodies MA-8H9D4 and MA-56A7C10, and their single-chain variable fragments (scFv), exhibit PAI-1-neutralizing properties. In this study, a rigid-body docking approach is used to predict the binding geometry of two distinct conformations of PAI-1 (active and latent) in complex with these antibody fragments. Resulting models were initially refined by using the dead-end elimination algorithm. Different filtering criteria based on the mutagenesis studies and structural considerations were applied to select the final models. These were refined by using the slow-cooling torsion-angle dynamic annealing protocol. The docked structures reveal the respective epitopes and paratopes and their potential interactions. This study provides crucial information that is necessary for the rational development of low-molecular weight PAI-1 inhibitors.     

Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differential expression (Open Access publication)

Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.     

Stem cell therapy applied for digestive anastomosis: Current state and future perspectives

BACKGROUND Digestive tract resections are usually followed by an anastomosis.Anastomotic leakage,normally due to failed healing,is the most feared complication in digestive surgery because it is associated with high morbidity and mortality.Despite technical and technological advances and focused research,its rates have remained almost unchanged the last decades.In the last two decades,stem cells(SCs)have been shown to enhance healing in animal and human studies;hence,SCs have emerged since 2008 as an alternative to improve anastomoses outcomes.AIM To summarise the published knowledge of SC utilisation as a preventative tool for hollow digestive viscera anastomotic or suture leaks.METHODS PubMed,Science Direct,Scopus and Cochrane searches were performed using the key words“anastomosis”,“colorectal/colonic anastomoses”,“anastomotic leak”,“stem cells”,“progenitor cells”,“cellular therapy”and“cell therapy”in order to identify relevant articles published in English and Spanish during the years of 2000 to 2021.Studies employing SCs,performing digestive anastomoses in hollow viscera or digestive perforation sutures and monitoring healing were finally included.Reference lists from the selected articles were reviewed to identify additional pertinent articles.METHODS Given the great variability in the study designs,anastomotic models,interventions(SCs,doses and vehicles)and outcome measures,performing a reliable meta-analysis was considered impossible,so we present the studies,their results and limitations.RESULTS Eighteen preclinical studies and three review papers were identified;no clinical studies have been published and there are no registered clinical trials.Experimental studies,mainly in rat and porcine models and occasionally in very adverse conditions such as ischaemia or colitis,have been demonstrated SCs as safe and have shown some encouraging morphological,functional and even clinical results.Mesenchymal SCs are mostly employed,and delivery routes are mainly local injections and cell sheets followed by biosutures(sutures coated by SCs)or purely topical.As potential weaknesses,animal models need to be improved to make them more comparable and equivalent to clinical practice,and the SC isolation processes need to be standardised.There is notable heterogeneity in the studies,making them difficult to compare.Further investigations are needed to establish the indications,the administration system,potential adjuvants,the final efficacy and to confirm safety and exclude definitively oncological concerns.CONCLUSION The future role of SC therapy to induce healing processes in digestive anastomoses/sutures still needs to be determined and seems to be currently far from clinical use.     

The insect‐focused classification of fruit syndromes in tropical rain forests: An inter‐continental comparison

We propose a new classification of rain forest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit‐feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand), and Wanang (Papua New Guinea). The three plots differed widely in fruit syndrome composition. Plant species with fleshy, indehiscent fruits containing multiple seeds were important at all three sites. However, in Panama, a high proportion of species had dry fruits, while in New Guinea and Thailand, species with fleshy drupes and thin mesocarps were dominant. Species with dry, winged seeds that do not develop as capsules were important in Thailand, reflecting the local importance of Dipterocarpaceae. These differences can also determine differences among frugivorous insect communities. Fruit syndromes and colors were phylogenetically flexible traits at the scale studied, as only three of the eight seed syndromes, and one of the 10 colors, showed significant phylogenetic clustering at either genus or family levels. Plant phylogeny was, however, the most important factor explaining differences in overall fruit syndrome composition among individual plant families or genera across the three study sites. Abstract in Melanesian is available with online material.     

Root herbivory in vitro: Interactions between roots and aphids grown in aseptic coculture

Summary An in vitro coculture system has been established to study interactions between roots and aphids. Eight aphid species (Aphis spiraecola P., Trama rara M., Macrosiphum euphorbiae S., Rhopalosiphum padi L., Sitobion avenae F., Rhopalosiphum maidis F., Metopolophium dirhodum W., and Pemphigus populivenae F.) were reared on six species of hairy root cultures, Carthamus tinctorius L. cv N10, Tagetes patula L., Trichosanthes cucumerina L. var anguina, Hyoscyamus muticus L., Nicotiana tabacum L., and Beta vulgaris L. subsp. vulgaris. All species of aphids survived on root cultures for at least 2 d. Three cocultures have been maintained aseptically for periods ranging from 2 mo. to over 2 yr. The coculture of R. padi on C. tinctorius cv N10 (N10-Rp) was used to study morphological and biochemical responses of roots under aphid herbivory. Aphid herbivory caused browning of cultures, reduced root vegetative growth, and increased production of polyacetylenes in C. tinctorius cv N10 roots. Our results suggest that this coculture system may improve our understanding of interactions between aphids and plant roots.     

Consequences of the reduction of plant diversity for litter decomposition: effects through litter quality and microenvironment

Decomposition of plant litter is a key process for the flow of energy and nutrients in ecosystems that may be sensitive to the loss of biodiversity. Two hypothetical mechanisms by which changes in plant diversity could affect litter decomposition are (1) through changes in litter species composition, and (2) by altering the decomposition microenvironment. We tested these ideas in relation to the short-term decomposition of herbaceous plant litter in experimental plant assemblages that differed in the numbers and types of plant species and functional groups that they contained to simulate loss of plant diversity. We used different litterbag experiments to separate the two potential pathways through which diversity could have an effect on decomposition. Our two litterbag trials showed that altering plant diversity affected litter breakdown differently through changes in decomposition microenvironment than through changes in litter composition. In the decomposition microenvironment experiment there was a significant but weak decline in decomposition rate in relation to decreasing plant diversity but no significant effect of plant composition. The litter composition experiment showed no effect of richness but significant effects of composition, including large differences between plant species and functional groups in litter chemistry and decomposition rate. However, for a nested subset of our litter mixtures decomposition was not accurately predicted from single-species bags; there were positive, non-additive effects of litter mixing which enhanced decomposition. We critically assess the strengths and limitations of our short-term litterbag trials in predicting the longer-term effects of changes in plant diversity on litter decomposition rates.     

Gut microbiota severely hampers the efficacy of NAD-lowering therapy in leukemia

Most cancer cells have high need for nicotinamide adenine dinucleotide (NAD⁺) to sustain their survival. This led to the development of inhibitors of nicotinamide (NAM) phosphoribosyltransferase (NAMPT), the rate-limiting NAD⁺ biosynthesis enzyme from NAM. Such inhibitors kill cancer cells in preclinical studies but failed in clinical ones. To identify parameters that could negatively affect the therapeutic efficacy of NAMPT inhibitors and propose therapeutic strategies to circumvent such failure, we performed metabolomics analyses in tumor environment and explored the effect of the interaction between microbiota and cancer cells. Here we show that tumor environment enriched in vitamin B3 (NAM) or nicotinic acid (NA) significantly lowers the anti-tumor efficacy of APO866, a prototypic NAMPT inhibitor. Additionally, bacteria (from the gut, or in the medium) can convert NAM into NA and thus fuel an alternative NAD synthesis pathway through NA. This leads to the rescue from NAD depletion, prevents reactive oxygen species production, preserves mitochondrial integrity, blunts ATP depletion, and protects cancer cells from death.Our data in an in vivo preclinical model reveal that antibiotic therapy down-modulating gut microbiota can restore the anti-cancer efficacy of APO866. Alternatively, NAphosphoribosyltransferase inhibition may restore anti-cancer activity of NAMPT inhibitors in the presence of gut microbiota and of NAM in the diet.Subject terms: Drug development, Cancer metabolism

     

The conservation and exploitation of vulnerable resources

The maximum principle of deterministic optimal control, which has proved to be a very useful tool in theoretical bioeconomics, is extended in this article to cover the optimal exploitation of a biological resource vulnerable to catastrophic collapse, the probability of which may depend in general on the state of the resource, the current control and time. A general formulation of the maximum principle for such stochastic problems is presented and a number of applications are outlined. These include: optimal harvesting of a fishery vulnerable to catastrophic collapse; optimal thinning of a forest vulnerable to fire; optimal expenditure and investment in forest fire protection and optimal consumption-pollution tradeoffs in an ecosystem vulnerable to pollution-related collapse. In addition an application of the method to a highly stylized behavioral ecology model is given.