Is Boron a Prebiotic Element? A Mini-review of the Essentiality of Boron for the Appearance of Life on Earth

Boron is probably a prebiotic element with special importance in the so-called "sugars world". Boron is not present on Earth in its elemental form. It is found only in compounds, e.g., borax, boric acid, kernite, ulexite, colemanite and other borates. Volcanic spring waters sometimes contain boron-based acids (e.g., boric, metaboric, tetraboric and pyroboric acid). Borates influence the formation of ribofuranose from formaldehyde that feeds the "prebiotic metabolic cycle". The importance of boron in the living world is strongly related to its implications in the prebiotic origins of genetic material; consequently, we believe that throughout the evolution of life, the primary role of boron has been to provide thermal and chemical stability in hostile environments. The complexation of boric acid and borates with organic cis-diols remains the most probable chemical mechanism for the role of this element in the evolution of the living world. Because borates can stabilize ribose and form borate ester nucleotides, boron may have provided an essential contribution to the "pre-RNA world".     

HuD Regulates the cpg15 Expression Via the 3′-UTR and AU-Rich Element

The candidate plasticity related gene 15 (cpg15) plays important roles in neural development and plasticity. In the present study, we studied the role of the cpg15 3′-untranslated region (UTR) in regulating the expression of the gene. The results showed that the presence of the 3′-UTR significantly decreases, while loss of a putative AU-rich element (ARE) in the 3′-UTR increases the cpg15 expression, indicating that the 3′-UTR and ARE may be essential for regulation of cpg15 expression. In addition, HuD, a neural-specific RNA binding protein, increased the cpg15 expression, which depends on the presence of the 3′-UTR and ARE. RNA-binding protein immunoprecipitation (RIP) assay demonstrated that HuD forms a complex with cpg15 mRNA in the cells of rat hippocampus. Deletion of HuD domains RRM1 plus RRM2 or Hinge region plus RRM3 attenuates the function of HuD in enhancing the cpg15 expression. The results suggest that HuD regulates the cpg15 expression via the 3′-UTR-mediated mechanism, which requires the presence of the ARE.     

Trace Element Concentration in Primary Liver Cancers—A Systematic Review

Background The incidence of primary liver cancer varies between countries. Many of the etiological factors contributing to the geographical variations in incidence are unknown. Development of hepatocellular carcinoma has been linked to levels of trace elements. This review summarizes the evidence associating HCC with trace elements. Methods MEDLINE, EMBASE, and CENTRAL databases were searched. Various inclusion and exclusion criteria were applied to select the articles for inclusion. Data extraction was performed using a custom designed data extraction form. Results A total of 12,344 references were identified. Duplicates, 1,597, were excluded. Clearly irrelevant references, 10,676, were excluded through reading titles and abstracts. Some references (59) were excluded by applying the exclusion criteria. Twelve studies including 646 patients and measuring iron content (8), copper content (11), zinc (9), and selenium (2) qualified for the review. Although a meta-analysis was not possible due to heterogeneity between the studies, a clear pattern of distribution of the trace elements was discernible. Conclusion Iron and zinc content are lower in HCC than in surrounding tissues or normal controls. Copper content is lower in HCC than in surrounding tissues and cirrhotic controls. Epidemiological and physiological reasons for the trace element alterations should be further investigated.     

A test for enhancement of cytotype regulation in Drosophila melanogaster by the transposase-encoding P Element ∆2-3

Transposable P elements are regulated in the germ line by piRNAs, which are small RNAs that associate with the Piwi class of proteins. This regulation, called the P cytotype, is enhanced by genetic interactions between P elements that are primary sources of these RNAs and other P elements. The enhanced regulation is thought to reflect amplification of the primary piRNAs by cleavage of mRNAs derived from the other P elements through a mechanism called the ping-pong cycle. We tested the transposase-encoding P element known as ?2-3 for its ability to enhance cytotype regulation anchored in P elements inserted at the telomere of the left arm of the X chromosome (TP elements). The ?2-3 P element lacks the intron between exons 2 and 3 in the structurally complete P element (CP). Unlike the CP element, it does not markedly enhance cytotype regulation anchored in TP elements, nor does it transmit transposase activity through the egg cytoplasm. However, mRNAs from both the CP and ?2-3 elements are maternally deposited in embryos. These observations suggest that maternally transmitted CP mRNA enhances cytotype regulation by participating in the ping-pong cycle and that it encodes the P transposase in the embryonic germ line, whereas maternally transmitted ?2-3 mRNA does not, possibly because it is not efficiently directed into the primordial embryonic germ line. Strong transposon regulation may, therefore, require ping-pong cycling with maternally inherited mRNAs in the embryo.     

Finite Element Modelling and Simulations in Dentistry: A Bibliography 1990–2003

The paper gives a bibliographical review of the finite element modelling and simulations in dentistry from the theoretical as well as practical points of view. The bibliography lists references to papers, conference proceedings and theses/dissertations that were published between 1990 and 2003. At the end of this paper, more than 700 references are given dealing with subjects such as: dental materials; oral and maxillofacial mechanics and surgery; orthodontics, tooth movement, orthodontic appliances; root canals, filling and therapy; dental restorations and other topics.     

Is Preventative Long-Segment Surgery for Multi-Level Spondylolysis Necessary? A Finite Element Analysis Study

Objective

For multi-level spondylolysis patients, surgeons commonly choose to fix all the segments with pars interarticularis defect even those without slippage and not responsible for clinical symptoms. In this study, we tried to study the necessity of the preventative long-segment surgery for the defected segment without slippage in treatment of multi-level spondylolysis patients from a biomechanical perspective.

Method

We established a bi-level spondylolysis model with pars defects at L4 and L5 segments, and simulated posterior lumbar interbody fusion (PLIF) and pedicle screw fixation at L5-S1 level. Then we compared the biomechanical changes at L4 segment before and after surgery in neutral, flexion, extension, lateral bending and axial rotation position.

Results

The stress on L4 pars interarticularis was very similar before and after surgery, and reached the highest in axial rotation. The L3-L4 intradiscal pressure was almost the same, while L4-L5 intradiscal pressure changed a little in lateral bending (increase from 1.993 to 2.160 MPa) and axial rotation (decrease from 1.639 to 1.307 MPa) after surgery. The PLIF surgery caused a little increase of range of motion at adjacent L4-L5 and L3-L4 levels, but the change is very tiny (1 degree).

Conclusion

The PLIF surgery will not cause significant biomechanical change at adjacent segment with pars defect in multi-level spondylolysis. On the contrary, excessive long-segment surgery will damage surrounding soft tissues which are important for maintaining the stability of spine. So a preventative long-segment surgery is not necessary for multi-level spondylolysis as long as there are no soft tissue degeneration signs at adjacent level.     

Spontaneous Excision of the Salmonella enterica Serovar Enteritidis-Specific Defective Prophage-Like Element φSE14

Salmonella enterica serovar Enteritidis has emerged as a major health problem worldwide in the last few decades. DNA loci unique to S. Enteritidis can provide markers for detection of this pathogen and may reveal pathogenic mechanisms restricted to this serovar. An in silico comparison of 16 Salmonella genomic sequences revealed the presence of an ∼12.5-kb genomic island (GEI) specific to the sequenced S. Enteritidis strain NCTC13349. The GEI is inserted at the 5′ end of gene ydaO (SEN1377), is flanked by 308-bp imperfect direct repeats (attL and attR), and includes 21 open reading frames (SEN1378 to SEN1398), encoding primarily phage-related proteins. Accordingly, this GEI has been annotated as the defective prophage SE14 in the genome of strain NCTC13349. The genetic structure and location of φSE14 are conserved in 99 of 103 wild-type strains of S. Enteritidis studied here, including reference strains NCTC13349 and LK5. Notably, an extrachromosomal circular form of φSE14 was detected in every strain carrying this island. The presence of attP sites in the circular forms detected in NCTC13349 and LK5 was confirmed. In addition, we observed spontaneous loss of a tetRA-tagged version of φSE14, leaving an empty attB site in the genome of strain NCTC13349. Collectively, these results demonstrate that φSE14 is an unstable genetic element that undergoes spontaneous excision under standard growth conditions. An internal fragment of φSE14 designated Sdf I has been used as a serovar-specific genetic marker in PCR-based detection systems and as a tool to determine S. Enteritidis levels in experimental infections. The instability of this region may require a reassessment of its suitability for such applications.The genus Salmonella comprises a heterogeneous group of Gram-negative bacteria, differentiable by biochemical and serological properties. More than 2,500 Salmonella serovars have been identified according to the serospecificities of the somatic and flagellar antigens. Some serovars, exemplified by Salmonella enterica serovar Typhimurium and S. Enteritidis, can infect a broad range of hosts. However, a subset of serovars, such as S. Typhi, a human-specific pathogen, show a high degree of adaptation to a specific host.In the last few decades, S. Enteritidis has emerged as a major health problem worldwide (31). This pathogen colonizes the reproductive organs of infected birds without causing discernible illness and survives host defenses during the formation of the egg (25, 27). The production of a capsule-like O antigen structure by certain wild-type strains of S. Enteritidis (30, 46) has been associated with reproductive tract tropism and improved survival within eggs (26, 27, 45). Egg contamination can originate before oviposition by direct contamination of the yolk, albumen, or eggshell membranes with bacteria from the infected reproductive organs of the birds or after or during oviposition by penetration of bacteria from contaminated feces through the eggshell (8, 14, 25). Transmission of the bacterium to humans occurs mainly through the consumption of contaminated eggs or egg products (8, 14, 25). Upon infection of a human host, S. Enteritidis causes self-limiting gastroenteritis similar to that caused by other nontyphoidal Salmonella serovars.According to information gathered from 84 countries responding to a global survey conducted by the World Health Organization (WHO), S. Enteritidis and S. Typhimurium accounted for ∼70% of all human and nonhuman isolates of Salmonella reported worldwide between 1995 and 2008. In fact, S. Enteritidis alone accounted for 61.4% of the ∼1.5 million human isolates of Salmonella reported during this period, according to the WHO Global Foodborne Infections Network Country Databank (http://www.who.int/salmsurv). Remarkably, S. Enteritidis is the second most prevalent cause of Salmonella infection in humans, after S. Typhimurium, in the United States (10).The high global prevalence of S. Enteritidis makes the development of a rapid, sensitive, and highly specific detection system critical to collect accurate epidemiologic data. The identification of loci that serve as specific markers for DNA-based identification of this pathogen may also provide insights into pathogenic mechanisms restricted to this serovar. Genomic regions that are unique to given serovars are especially suitable for such epidemiologic detection (3). For instance, Agron and colleagues identified an S. Enteritidis-specific genomic region of ∼4,060 bp adjacent to the ydaO gene, carrying six open reading frames (ORFs) that they designated lygA to lygF (1). A PCR-based assay successfully detected the presence of an internal fragment of this serovar-specific region in most strains in a diverse collection of clinical and environmental S. Enteritidis isolates and not in 73 non-Enteritidis isolates of S. enterica representing 34 different serovars (1). Since then, this region has been widely used as an S. Enteritidis-specific molecular marker in the development of several PCR-based assays for detection and epidemiological typing of Salmonella serovars in clinical and environmental samples (2, 11, 32, 37, 44, 53). Recently, an S. Enteritidis-specific real-time quantitative PCR (qPCR) assay based on the detection of this region was developed (15). This qPCR assay has been used in a series of studies of the distribution and replication kinetics of S. Enteritidis in experimentally infected animals (16-21).We performed a bioinformatic study to identify genomic regions specific to S. Enteritidis and found a genomic island (GEI) that includes the S. Enteritidis-specific locus lyg (1). This island has been annotated as the defective prophage SE14 in the genome of S. Enteritidis strain NCTC13349 (52). Although we demonstrate that the location in the genome and the overall genetic structure of the island are conserved in wild-type isolates of S. Enteritidis from different origins, we detected strains that do not carry the island in their genomes. Finally, we demonstrate here that the island corresponds to an unstable element that undergoes spontaneous excision from the genome of S. Enteritidis under standard growth conditions.     

An RNA Element at the 5′-End of the Poliovirus Genome Functions as a General Promoter for RNA Synthesis

RNA structures present throughout RNA virus genomes serve as scaffolds to organize multiple factors involved in the initiation of RNA synthesis. Several of these RNA elements play multiple roles in the RNA replication pathway. An RNA structure formed around the 5′- end of the poliovirus genomic RNA has been implicated in the initiation of both negative- and positive-strand RNA synthesis. Dissecting the roles of these multifunctional elements is usually hindered by the interdependent nature of the viral replication processes and often pleiotropic effects of mutations. Here, we describe a novel approach to examine RNA elements with multiple roles. Our approach relies on the duplication of the RNA structure so that one copy is dedicated to the initiation of negative-strand RNA synthesis, while the other mediates positive-strand synthesis. This allows us to study the function of the element in promoting positive-strand RNA synthesis, independently of its function in negative-strand initiation. Using this approach, we demonstrate that the entire 5′-end RNA structure that forms on the positive-strand is required for initiation of new positive-strand RNAs. Also required to initiate positive-strand RNA synthesis are the binding sites for the viral polymerase precursor, 3CD, and the host factor, PCBP. Furthermore, we identify specific nucleotide sequences within “stem a” that are essential for the initiation of positive-strand RNA synthesis. These findings provide direct evidence for a trans-initiation model, in which binding of proteins to internal sequences of a pre-existing positive-strand RNA affects the synthesis of subsequent copies of that RNA, most likely by organizing replication factors around the initiation site.     

Finite Element Analysis of the Cingulata Jaw: An Ecomorphological Approach to Armadillo’s Diets

Finite element analyses (FEA) were applied to assess the lower jaw biomechanics of cingulate xenarthrans: 14 species of armadillos as well as one Pleistocene pampathere (11 extant taxa and the extinct forms Vassallia, Eutatus and Macroeuphractus). The principal goal of this work is to comparatively assess the biomechanical capabilities of the mandible based on FEA and to relate the obtained stress patterns with diet preferences and variability, in extant and extinct species through an ecomorphology approach. The results of FEA showed that omnivorous species have stronger mandibles than insectivorous species. Moreover, this latter group of species showed high variability, including some similar biomechanical features of the insectivorous Tolypeutes matacus and Chlamyphorus truncatus to those of omnivorous species, in agreement with reported diets that include items other than insects. It remains unclear the reasons behind the stronger than expected lower jaw of Dasypus kappleri. On the other hand, the very strong mandible of the fossil taxon Vassallia maxima agrees well with the proposed herbivorous diet. Moreover, Eutatus seguini yielded a stress pattern similar to Vassalia in the posterior part of the lower jaw, but resembling that of the stoutly built Macroeuphractus outesi in the anterior part. The results highlight the need for more detailed studies on the natural history of extant armadillos. FEA proved a powerful tool for biomechanical studies in a comparative framework.