Growth of bifidobacteria and clostridia on human and cow milk saccharides

For healthy infants, which were born normally and fully breastfed, the dominant component of the intestinal microflora are bifidobacteria. However, infants born by caesarean section possess clostridia as a dominant intestinal bacterial group. The aim of the present study was to determine whether bifidobacteria and clostridia are able to grow on human milk oligosaccharides (HMOs) and other carbon sources - lactose, cow milk (CM) and human milk (HM). Both bifidobacteria and clostridia grew on lactose and in CM. Bifidobacteria grew in HM and on HMOs. In contrast, 3 out of 5 strains of clostridia were not able to grow in HM. No clostridial strain was able to utilise HMOs. While both bifidobacterial strains were resistant to lysozyme, 4 out of 5 strains of clostridia were lysozyme-susceptible. It seems that HMOs together with lysozyme may act as prebiotic-bifidogenic compounds inhibiting intestinal clostridia.     

Fungal laccases - occurrence and properties

Laccases of fungi attract considerable attention due to their possible involvement in the transformation of a wide variety of phenolic compounds including the polymeric lignin and humic substances. So far, more than a 100 enzymes have been purified from fungal cultures and characterized in terms of their biochemical and catalytic properties. Most ligninolytic fungal species produce constitutively at least one laccase isoenzyme and laccases are also dominant among ligninolytic enzymes in the soil environment. The fact that they only require molecular oxygen for catalysis makes them suitable for biotechnological applications for the transformation or immobilization of xenobiotic compounds.     

Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines

Transgelin is a protein reported to be a marker of several cancers. However, previous studies have shown both up‐ and down‐regulation of transgelin in tumors when compared with non‐tumor tissues and the mechanisms whereby transgelin may affect the development of cancer remain largely unknown. Transgelin is especially abundant in smooth muscle cells and is associated with actin stress fibers. These contractile structures participate in cell motility, adhesion, and the maintenance of cell morphology. Here, the role of transgelin in breast cancer is focused on. Initially, the effects of transgelin on cell migration of the breast cancer cell lines, BT 549 and PMC 42, is studied. Interestingly, transgelin silencing increased the migration of PMC 42 cells, but decreased the migration of BT 549 cells. To clarify these contradictory results, the changes in protein abundances after transgelin silencing in these two cell lines are analyzed using quantitative proteomics. The results confirmed the role of transgelin in the migration of BT 549 cells and suggest the involvement of transgelin in apoptosis and small molecule biochemistry in PMC 42 cells. The context‐dependent function of transgelin reflects the different molecular backgrounds of these cell lines, which differ in karyotypes, mutation statuses, and proteome profiles.     

The biogeography of naturalization in alien plants

Aim  This paper reviews the main geographical determinants of naturalization in plants.
Location  Global.
Methods  Comparative studies of large data sets of alien floras are the main source of information on global patterns of naturalization.
Results  Temperate mainland regions are more invaded than tropical mainland regions but there seems to be no difference in invasibility of temperate and tropical islands. Islands are more invaded than the mainland. The number of naturalized species in temperate regions decreases with latitude and their geographical ranges increase with latitude. The number of naturalized species on islands increases with temperature. Naturalized species contribute to floristic homogenization, but the phenomenon is scale-dependent.
Main conclusions  Some robust patterns are evident from currently available data, but further research is needed on several aspects to advance our understanding of the biogeography of naturalization of alien plants. For example, measures of propagule pressure are needed to determine the invasibility of communities/ecosystems/regions. The patterns discussed in this paper are derived largely from numbers and proportions of naturalized species, and little is known about the proportion of introduced species that become naturalized. Further insights on naturalization rates, i.e. the proportion of aliens that successfully naturalize within regions, and on geographical and other determinants of its variation would provide us with better understanding of the invasion process. Comparative studies, and resulting generalizations, are almost exclusively based on numbers of species, but alien species differ in their impact on native biodiversity and ecosystem processes.     

Firmicutes is an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs,Western Siberia,Russia

The dominant microbial components of fluids from wells in pristine and water-injected, high-temperature, Western Siberian oil fields, were analyzed by PCR-DGGE. Particular emphasis was placed on sulphate-reducing organisms, due to their ecological and industrial importance. Bacterial phylotypes obtained from the non-water-injected Stolbovoye oil field were more diverse than those from the Samotlor field, which is subject to secondary oil recovery by reinjection of recycled production water. The majority of phylotypes from both sites were related to Firmicutes. The low similarity to their closest relatives indicates unique bacterial communities in deep underground production waters and crude oil. Archaeal phylotypes detected only in the Samotlor samples were represented by Methanosarcinales and Methanobacteriales.     

Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus

Spontaneous damage to DNA as a result of deamination, oxidation and depurination is greatly accelerated at high temperatures. Hyperthermophilic microorganisms constantly exposed to temperatures exceeding 80°C are endowed with powerful DNA repair mechanisms to maintain genome stability. Of particular interest is the processing of DNA lesions during replication, which can result in fixed mutations. The hyperthermophilic crenarchaeon Sulfolobus solfataricus has two functional DNA polymerases, PolB1 and PolY1. We have found that the replicative DNA polymerase PolB1 specifically recognizes the presence of the deaminated bases hypoxanthine and uracil in the template by stalling DNA polymerization 3–4 bases upstream of these lesions and strongly associates with oligonucleotides containing them. PolB1 also stops at 8-oxoguanine and is unable to bypass an abasic site in the template. PolY1 belongs to the family of lesion bypass DNA polymerases and readily bypasses hypoxanthine, uracil and 8-oxoguanine, but not an abasic site, in the template. The specific recognition of deaminated bases by PolB1 may represent an initial step in their repair while PolY1 may be involved in damage tolerance at the replication fork. Additionally, we reveal that the deaminated bases can be introduced into DNA enzymatically, since both PolB1 and PolY1 are able to incorporate the aberrant DNA precursors dUTP and dITP.     

Evolution of a new enzyme activity from the same motif fold

The host cell recognition protein of the Escherichia coli bacteriophage HK620 is a large homotrimeric tailspike that cleaves the O18A1 type O antigen. The crystal structure of HK620 tailspike determined in the apo and substrate-bound form is reported by Barbirz et al. in this issue of Molecular Microbiology. Lacking detectable sequence similarity, the fold and overall organization of the HK620 tailspike are similar to those of the tailspikes of the related phages P22 and Sf6. The substrate-binding site is intrasubunit in P22 and HK620 tailspikes, but intersubunit in Sf6, demonstrating how phages can adapt the same protein fold to recognize different substrates.     

On the possibility of identifying human subjects using behavioural complexity analyses

Background: Identification of human subjects using a geometric approach to complexity analysis of behavioural data is designed to provide a basis for a more precise diagnosis leading towards personalised medicine. Methods: The approach is based on capturing behavioural time-series that can be characterized by a fractional dimension using non-invasive longer-time acquisitions of heart rate, perfusion, blood oxygenation, skin temperature, relative movement and steps frequency. The geometry based approach consists in the analysis of the area and centroid of convex hulls encapsulating the behavioural data represented in Euclidian index spaces based on the scaling properties of the self-similar normally distributed behavioural time-series of the above mentioned quantities. Results: An example demonstrating the presented approach of behavioural fingerprinting is provided using sensory data of eight healthy human subjects based on approximately fifteen hours of data acquisition. Our results show that healthy subjects can be factorized to different similarity groups based on a particular choice of a convex hull in the corresponding Euclidian space. One of the results indicates that healthy subjects share only a small part of the convex hull pertaining to a highly trained individual from the geometric comparison point of view. Similarly, the presented pair-wise individual geometric similarity measure indicates large differences among the subjects suggesting the possibility of neuro-fingerprinting. Conclusions: Recently introduced multi-channel body-attached sensors provide a possibility to acquire behavioural time-series that can be mathematically analysed to obtain various objective measures of behavioural patterns yielding behavioural diagnoses favouring personalised treatments of, e.g., neuropathologies or aging.