Animal Rennets as Sources of Dairy Lactic Acid Bacteria

The microbial composition of artisan and industrial animal rennet pastes was studied by using both culture-dependent and -independent approaches. Pyrosequencing targeting the 16S rRNA gene allowed to identify 361 operational taxonomic units (OTUs) to the genus/species level. Among lactic acid bacteria (LAB), Streptococcus thermophilus and some lactobacilli, mainly Lactobacillus crispatus and Lactobacillus reuteri, were the most abundant species, with differences among the samples. Twelve groups of microorganisms were targeted by viable plate counts revealing a dominance of mesophilic cocci. All rennets were able to acidify ultrahigh-temperature-processed (UHT) milk as shown by pH and total titratable acidity (TTA). Presumptive LAB isolated at the highest dilutions of acidified milks were phenotypically characterized, grouped, differentiated at the strain level by randomly amplified polymorphic DNA (RAPD)-PCR analysis, and subjected to 16S rRNA gene sequencing. Only 18 strains were clearly identified at the species level, as Enterococcus casseliflavus, Enterococcus faecium, Enterococcus faecalis, Enterococcus lactis, Lactobacillus delbrueckii, and Streptococcus thermophilus, while the other strains, all belonging to the genus Enterococcus, could not be allotted into any previously described species. The phylogenetic analysis showed that these strains might represent different unknown species. All strains were evaluated for their dairy technological performances. All isolates produced diacetyl, and 10 of them produced a rapid pH drop in milk, but only 3 isolates were also autolytic. This work showed that animal rennet pastes can be sources of LAB, mainly enterococci, that might contribute to the microbial diversity associated with dairy productions.     

Quirks of dye nomenclature. 5. Rhodamines

Rhodamines were first produced in the late 19^th century, when they constituted a new class of synthetic dyes. These compounds since have been used to color many things including cosmetics, inks, textiles, and in some countries, food products. Certain rhodamine dyes also have been used to stain biological specimens and currently are widely used as fluorescent probes for mitochondria in living cells. The early history and current biological applications are sketched briefly and an account of the ambiguities, complications and confusions concerning dye identification and nomenclature are discussed.     

Oxidatively-modified and glycated proteins as candidate pro-inflammatory toxins in uremia and dialysis patients

End stage renal disease (ESRD) patients accumulate blood hallmarks of protein glycation and oxidation. It is now well established that these protein damage products may represent a heterogeneous class of uremic toxins with pro-inflammatory and pro-oxidant properties. These toxins could be directly involved in the pathogenesis of the inflammatory syndrome and vascular complications, which are mainly sustained by the uremic state and bioincompatibility of dialysis therapy. A key underlying event in the toxicity of these proteinaceous solutes has been identified in scavenger receptor-dependent recognition and elimination by inflammatory and endothelial cells, which once activated generate further and even more pronounced protein injuries by a self-feeding mechanism based on inflammation and oxidative stress-derived events. This review examines the literature and provides original information on the techniques for investigating proteinaceous pro-inflammatory toxins. We have also evaluated therapeutic - either pharmacological or dialytic - strategies proposed to alleviate the accumulation of these toxins and to constrain the inflammatory and oxidative burden of ESRD.     

The role of the integral membrane nucleoporins Ndc1p and Pom152p in nuclear pore complex assembly and function

The nuclear pore complex (NPC) is a large channel that spans the two lipid bilayers of the nuclear envelope and mediates transport events between the cytoplasm and the nucleus. Only a few NPC components are transmembrane proteins, and the role of these proteins in NPC function and assembly remains poorly understood. We investigate the function of the three integral membrane nucleoporins, which are Ndc1p, Pom152p, and Pom34p, in NPC assembly and transport in Saccharomyces cerevisiae. We find that Ndc1p is important for the correct localization of nuclear transport cargoes and of components of the NPC. However, the role of Ndc1p in NPC assembly is partially redundant with Pom152p, as cells lacking both of these proteins show enhanced NPC disruption. Electron microscopy studies reveal that the absence of Ndc1p and Pom152p results in aberrant pores that have enlarged diameters and lack proteinaceous material, leading to an increased diffusion between the cytoplasm and the nucleus.     

Application of an optimized marker amplification protocol in immunohistochemistry — a valuable tool for visualizing antigenic sites of low signal strength or sparse distribution

Amplification of immunohistochemical markers received considerable attention during the 1980s and 1990s. The amplification approach was largely abandoned following the development of antigen retrieval and reporter amplification techniques, because the latter were incorporated more easily into high throughput automated procedures in industrial and diagnostic laboratories. There remain, however, a number of instances where marker amplification still has much to offer. Consequently, we examined experimentally the utility of an optimized marker amplification technique in diagnostically relevant tissue where either the original signal strength was low or positive sites were visible, but sparsely distributed. Marker amplification in the former case not only improved the visibility of existing positive sites, but also revealed additional sites that previously were undetectable. In the latter case, positive sites were rendered more intense and therefore more easily seen during low magnification examination of large areas of tissue.     

Comparison of lipoteichoic acid from different serotypes of Streptococcus pneumoniae

Pneumococcal lipoteichoic acid (LTA) is known to have a completely different chemical structure compared with that of Staphylococcus aureus: the polyglycerophosphate in the backbone is replaced in the pneumococcal LTA by a pentamer repeating unit consisting of one ribitol and a tetrasaccharide carrying the unusual substituents phosphocholine and N-acetyl-D-galactosamine. Neither D-alanine nor N-acetyl-D-glucosamine, which play central roles in the biological activity of the staphylococcal LTA, has been reported. The extraction using butanol is more gentle compared with the previously reported chloroform-methanol extraction and results in a higher yield of LTA. We characterized the LTA of two different strains of Streptococcus pneumoniae:R6 (serotype 2) and Fp23 (serotype 4). NMR analysis confirmed the structure of LTA from R6 but showed that its ribitol carries an N-acetyl-D-galactosamine substituent. The NMR data for the LTA from Fp23 indicate that this LTA additionally contains ribitol-bound D-alanine. Dose-response curves of the two pneumococcal LTAs in human whole blood revealed that LTA from Fp23 was significantly more potent than LTA from R6 with regard to the induction of all cytokines measured (tumor necrosis factor, interleukin-1 (IL-1), IL-8, IL-10, granulocyte colony-stimulating factor, and interferon gamma). However, other characteristics, such as lack of inhibition by endotoxin-specific LAL-F, Toll-like receptor 2 and not 4 dependence, and lack of stimulation of neutrophilic granulocytes, were shared by both LTAs. This is the first report of a difference in the structure of LTA between two pneumococcal serotypes resulting in different immunostimulatory potencies.     

Mitigation of copper toxicity by DNA oligomers in green paramecia

Impact of transition metals which catalyze the generation of reactive oxygen species (ROS), on activation of cell death signaling in plant cells have been documented to date. Similarly in green paramecia (Paramecium bursaria), an aquatic protozoan species harboring symbiotic green algae in the cytoplasm, toxicities of various metallic ions have been documented. We have recently examined the effects of double-stranded GC-rich DNA fragments with copper-binding nature and ROS removal catalytic activity as novel plant cell-protecting agents, using the suspension-cultured tobacco cells. Here, we show that above DNA oligomers protect the cells of green paramecia from copper-induced cell death, suggesting that the phenomenon firstly observed in tobacco cells is not limited only within higher plants but it could be universally observable in wider range of organisms.     

Combined exposure to cigarette smoke and nontypeable Haemophilus influenzae drives development of a COPD phenotype in mice

Background

Cigarette smoke (CS) is the major etiologic factor of chronic obstructive pulmonary disease (COPD). CS-exposed mice develop emphysema and mild pulmonary inflammation but no airway obstruction, which is also a prominent feature of COPD. Therefore, CS may interact with other factors, particularly respiratory infections, in the pathogenesis of airway remodeling in COPD.

Methods

C57BL/6 mice were exposed to CS for 2 h a day, 5 days a week for 8 weeks. Mice were also exposed to heat-killed non-typeable H. influenzae (HK-NTHi) on days 7 and 21. One day after the last exposure to CS, mice were sacrificed and lung inflammation and mechanics, emphysematous changes, and goblet cell metaplasia were assessed. Mice exposed to CS or HK-NTHi alone or room air served as controls. To determine the susceptibility to viral infections, we also challenged these mice with rhinovirus (RV).

Results

Unlike mice exposed to CS or HK-NTHi alone, animals exposed to CS/HK-NTHi developed emphysema, lung inflammation and goblet cell metaplasia in both large and small airways. CS/HK-NTHi-exposed mice also expressed increased levels of mucin genes and cytokines compared to mice in other groups. CS/HK-NTHi-exposed mice infected with RV demonstrated increased viral persistence, sustained neutrophilia, and further increments in mucin gene and chemokine expression compared to other groups.

Conclusions

These findings indicate that in addition to CS, bacteria may also contribute to development of COPD, particularly changes in airways. Mice exposed to CS/HK-NTHi are also more susceptible to subsequent viral infection than mice exposed to either CS or HK-NTHi alone.     

Anomalie Anatomiche NEL Legno DI Rami DI Ciliegio Sottoposti a Defogliazione

Summary

The Author studies the secondary wood in a Cherry tree «Regina del Mercato» and describes several degenerative factures in the wood elements.

The author concludes that there is a close relation between number and development of the leaves and differentiation of secondary wood elements.     

Plant Neurobiology as a Paradigm Shift Not Only in the Plant Sciences

Plants are complex living beings, extremely sensitive to environmental factors, continuously adapting to the ever changing environment. Emerging research document that plants sense, memorize, and process experiences and use this information for their adaptive behavior and evolution. As any other living and evolving systems, plants act as knowledge accumulating systems. Neuronal informational systems are behind this concept of organisms as knowledge accumulating systems because they allow the most rapid and efficient adaptive responses to changes in environment. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants. The journal, Plant Signaling & Behavior, was launched as a platform for exchanging information and fostering research on plant neurobiology in order to allow our understanding of plants in their whole integrated, communicative, and behavioral complexity.

I always go by official statistics because they are very carefully compounded and, even if they are false, we have no others …∼ Jaroslav Hašek, 1911

Key Words: plant neurobiology, sensory biology, behavior, biological complexity, evolution, signal integrationThis quotation of writer and mystificator Jaroslav Hašek is from his electorial speech aimed to get a seat in the Austro-Hungarian parliament for his imaginary political party ‘Moderate Progress within the Limits of the Law’ in 1911. It indicates how statistics can be misused for manipulation of public opinion, sometimes allegedly for general good. This quotation is partially relevant also for recent biology which is passing through a critical cross-road from reductionist-mechanistic concepts and methodologies towards the post-genomic, holistic, systems-based analysis of integrated and communicative hierarchic networks known as life processes.There is a message hidden in this Hašek''s aphorism. All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.¹Despite the indisputable success of the reductionistic approach in providing many discoveries regarding single cells and their components, it is increasingly clear that promises of ‘mechanistic’ genocentric biology were just chimeras and that living organisms are much more complex than the sum of their constituents. Ernst Mayr, in his final opus, almost a testament published at his age of 100, strongly opposed the belief that the reductionism at the molecular level could help to explain the complexity of life. He stressed that the concept of biological “emergence”, which deals with the occurrence of unexpected features in complex living systems, is not fully accessible using only physical and chemical approaches.²Themes of hierarchy, continuity, and order dominated biology before the turn of the century, but these have in many cases been replaced by images of the workshop. Examples include such terms as ‘machineries’, ‘mechanistic understanding’, ‘mechanistic explanation’, ‘motors’, ‘machines’, ‘clocks’ etc. This shift may well reflect the characteristic style of our age. These concepts, although useful for mining of details, do not reveal the true complexity of life and can be misleading. Even a one-celled organism is made up of ‘millions’ of subcellular parts. Concerning the great complexity of unicellular creatures Ilya Prigogine (1973) wrote: “… but let us have no illusions, our research would still leave us quite unable to grasp the extreme complexity of the simplest of organism.”³ Moreover, eukaryotic cell proved to be, in fact, ‘cells within cell’,^4–8 while there are numerous supracellular situations, the most dramatic one is represented by plants when all cells are interconnected via plasmodesmata into supracellular organism.⁶ All this collectively indicate that the currently valid ‘Cell Theory’ dogma is approaching its replacement with a new updated concept of a basic unit of eukaryotic life.^6–8All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.Furthermore, genomes are much more complex and dynamic as we ever anticipated.^9,10 They often have as much as 99% of non-coding DNA sequences,¹¹ which is not ‘junk DNA’ but rather DNA which is part of multitask networks integrating coding DNA.¹² In genomes exposed to stress (like mutations), changes are scored preferentially in non-coding sequences which regain a new balance by complex changes in genome composition and activity.^9,10,13,14 There are several definitions regarding what is gene¹¹ and molecular biologists and genetics are learning to be careful not to make strong conclusions from under-expression, knocking-out, or overexpression of any particular gene. It is increasingly clear that mutations in single genes are accompanied with altered expressions of other genes and non-coding DNA sequences too, and even subtle re-arrangements of chromatin structure and genome architecture are possible. The dynamic genome actively regains the lost balance, also via extensive re-shufflings of non-coding DNA.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of the genomics era some 60 years ago. Yet, it is also obvious that living systems, whether single cells or whole complex organisms like animals and plants, are not machines and automata which respond to external signals via a limited set of predefined responses and automatic reflexes. While humans and other animals, even insects, are already out of this ‘mechanistic’ trap^15,16 which can be traced back to Descartes,¹⁷ plants are still considered to act only in predetermined automatic fashions, as mechanical devices devoid of any possibility for choice and planning of their activities. In contrast to machines, life systems are based on wet chemistry, being systems of hierarchical and dynamic integration, communication and emergence.^1,18Recently, a critical mass of data has accumulated demanding reconsideration of this mechanistic view of plants.^19,20 Plants are complex living beings, extremely sensitive to environmental factors and continuously adapting to the ever changing environment.²¹ In addition, plants respond to environmental stimuli as integrated organisms. Often, plants make important decisions, such as onset or breakage of dormancy and onset of flowering, which implicate some central or decentralized command center. Moreover, roots and shoots act in an integrated manner allowing dynamic balance of above-ground and below-ground organs. The journal, Plant Signaling & Behavior, was launched as a platform for exchange of information about the integration of discrete processes, including subcellular signalling integrated with higher-level processes. Signal integration and communication results in adaptive behavior of whole supracellular organisms, encompassing also complex, and still elusive, plant-plant, plant-insect, and plant-animal communications. Coordinated behavior based on sensory perception is inherent for neurobiological systems.²² Therefore, plants can be considered for neuronal individuals. Moreover, plants are also able to share knowledge perceived from environment with other plants, communicating both private and public messages.^23,24 This implicates social learning and behavioral inheritance in plants too.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of genomics era some 60 years ago.

Behavior

1. An activity of a defined organism: observable activity when measurable in terms of quantitative effects of the environment whether arising from internal or external stimuli.
2. Anything that an organism does that involves action and response to stimulation.

(Webster Third New International Dictionary 1961).Neuronal informational systems allow the most rapid and efficient adaptive responses. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants.Some of our colleagues assert that plants do not exhibit any integrated neuronal principles.²⁵ They maintain that plants do not show complex experience- or learning-based behavior. Plants, they aver, act rather as machines manifesting predefined reflexes. Yet recent studies indicate that even prokaryotic bacteria exhibit cognitive behavior^26,27 and posses linguistic communication and rudimentary intelligence.^28–30 Therefore, it should not be too surprising that plants also show features of communication and even plant-specific cognition.^{19,20,31,32–35} As any other living systems, plants act as ‘knowledge accumulating systems’.¹ In fact, in order to adapt, all organisms continuously generate hypotheses about their environment via well formulated ‘questions’ which are solved by an increasing set of possible ‘answers’ in order to adapt.¹ Neuronal informational systems are behind this concept of organisms as ‘knowledge accumulating systems’ because they allow the most rapid and efficient adaptive responses.²² As a consequence, neuronal computation is not limited to animal brains but is used also by bacteria and plants.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior. We trust that Plant Signaling & Behavior, will become an important platform for exchange of these ideas. With progress of sciences, plants show more and more similarities to animals despite obviously plant-specific evolutionary origins, cellular basis, and multicellularity. We can just mention sexuality and sex organs, embryos, stem cells, immunity, circadian rhythms, hormonal and peptide signaling, sensory perception and bioelectricity including action potentials, communication and neurobiological aspects of signal integration. The whole picture strongly suggest that convergent evolution is much more important^36,37 than currently envisioned in evolutionary theories.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior.We have started with Jaroslav Hašek and we close with him as well. His quotation from 1911 is also a warning for future that we should stay open-minded. We should not slip into dogmatic ‘traps’ which have been so characteristic for the mechanistic and genocentric biology. Mathematics and computational biology are important tools, and surely will play decisive role in systems biology in the future. But they can be easily misinterpreted, and even misused. Plant systems biology, and the whole biology in general, must overcome dogmas of mechanistic genocentric biology. We hope that characterizing plants in their whole behavioral and communicative complexity will allow us to better understand what is life and how it emerged from chemical and biochemical complex systems.