Connecting chemical worlds for a sustainable future

Chemistry plays a central role in science and is the basis of one of the major, more impactful, and diverse industries. However, to address the most pressing global challenges, we must learn to create connections in an effective and meaningful way, with other disciplines, industries, and society at large. Here, we present the IUPAC Top Ten Emerging Technologies in Chemistry as an example of an initiative that highlights the value of the most promising advances in chemistry and contributes to creating connections to accelerate sustainable solutions for our society and our planet.

Language of Chemistry: Making IUPAC Nomenclature Available in Spanish

Science, including mathematics, physics, and, of course, chemistry, has its own language and symbols and names we learn in school. However, to teach it, communicate it, and use it, we use our own native languages. Most of the scientific literature, including this article, is in English, as are the texts published by the various scientific unions, including the International Union of Pure and Applied Chemistry (IUPAC), to define scientific nomenclature, terminology, and presentation. However, it is essential that these fundamental texts are available in as many languages as possible to facilitate their teaching, learning, and use throughout the world. It should be noted, however, that the translation of these texts into different languages is a complex task that requires some choices due to the lack of obvious alternatives or the cacophony of some terms. In this paper, we provide some details on the challenges, compromises, and difficult decisions involved in translating the IUPAC Nomenclature Brief Guides into Spanish.

Pharmacogenetic biomarkers for secukinumab response in psoriasis patients in real-life clinical practice

BACKGROUND

Prediction of the response to a biological treatment in psoriasis patients would allow efficient treatment allocation.

OBJECTIVE

To identify polymorphisms associated with secukinumab response in psoriasis patients in a daily practice setting.

METHODS

We studied 180 SNPs in patients with moderate-to-severe plaque psoriasis recruited from 15 Spanish hospitals. Treatment effectiveness was evaluated by absolute PASI ≤3 and ≤1 at 6 and 12 months. Individuals were genotyped using a custom Taqman array. Multiple logistic regression models were generated. Sensitivity, specificity and area under the curve (AUC) were analysed.

RESULTS

A total of 173 patients were studied at 6 months, (67% achieved absolute PASI ≤ 3 and 65% PASI ≤ 1) and 162 at 12 months (75% achieved absolute PASI ≤ 3 and 64% PASI ≤ 1). Multivariable analysis showed the association of different sets of SNPs with the response to secukinumab. The model of absolute PASI≤3 at 6 months showed best values of sensitivity and specificity. Four SNPs were associated with the capability of achieving absolute PASI ≤ 3 at 6 months. rs1801274 (FCGR2A), rs2431697 (miR-146a) and rs10484554 (HLCw6) were identified as risk factors for failure to achieve absolute PASI≤3, while rs1051738 (PDE4A) was protective. AUC including these genotypes, weight of patients and history of biological therapy was 0.88 (95% CI 0.83-0.94), with a sensitivity of 48.6% and specificity of 95.7% to discriminate between both phenotypes.

CONCLUSION

We have identified a series of polymorphisms associated with the response to secukinumab capable of predicting the potential response/non-response to this drug in patients with plaque psoriasis.

Blue-LED activated photocatalytic hydrogenation of nitroarenes with Cu2O/CuO heterojunctions

This study describes how the optimization of Cu2O/CuO heterostructures can enhance their (photo)catalytic performance. More specifically, the evaluation of catalysts with different Cu2O/CuO molar ratios was used to optimize their performance for the hydrogenation of 4-nitrophenol under both blue-LED light and dark conditions. For the first time, we analyzed the effect of blue LED irradiation on this reaction and found that when blue LEDs are used as the light source, a Cu2O/CuO ratio of 0.15 results in rate constants 7 to 3 times higher than those of catalysts with either lower (0.01) or higher (0.42) ratios. Furthermore, this photocatalyst shows good stability, >70% after 5 cycles, and excellent chemoselectivity in the selective reduction of the nitro group in the presence of other functionalities, i.e. -COOH, -CONH2 and -OH.

Chemical Solutions to the Current Polycrisis

In the past 15 years, we've experienced an unprecedented series of crises, including financial (2008), health (2020), and most recently the supply chain disruptions and the energy emergency in Europe, caused by the war in Ukraine (2022). On top of that, climate change still poses a serious threat to our lives and our planet. These interconnected challenges create tremendous societal problems and compromise the viability of the chemical industry in an environment of price volatility and high inflation. Thus, the International Union of Pure and Applied Chemistry (IUPAC) has launched a series of actions to tackle this and raise awareness of the role of chemistry in solving our major threats. Since 2019, IUPAC has identified the "Top Ten Emerging Technologies in Chemistry" to connect chemical researchers with industry, bridging the gap between science and innovation, maintaining the current competitiveness of the chemical industry, as well as tackling our most pressing global challenges.

Tunable hybrid zeolites prepared by partial interconversion

Zeolite interconversion is a widely used strategy due to its unique advantages in the synthesis of some zeolites. By using a long-chain quaternary amine as both a structure-directing agent and porogen, we have produced superior catalysts, which we named Hybrid Zeolites, as their structures are made of building units of different zeolite types. The properties of these materials can be conveniently tuned, and their catalytic performance can be optimized simply by stopping the interconversion at different times. For cracking the 1,3,5-triisopropylbenzene, Hybrid Zeolites made of FAU and MFI units show a 5-fold increase in selectivity towards the desired product, that is, 1,3-diisopropylbenzene, compared to the commercial FAU, and a 7-fold increase in conversion at constant selectivity compared to MFI zeolite.

How Reproducible are Surface Areas Calculated from the BET Equation?

Porosity and surface area analysis play a prominent role in modern materials science. At the heart of this sits the Brunauer-Emmett-Teller (BET) theory, which has been a remarkably successful contribution to the field of materials science. The BET method was developed in the 1930s for open surfaces but is now the most widely used metric for the estimation of surface areas of micro- and mesoporous materials. Despite its widespread use, the calculation of BET surface areas causes a spread in reported areas, resulting in reproducibility problems in both academia and industry. To prove this, for this analysis, 18 already-measured raw adsorption isotherms were provided to sixty-one labs, who were asked to calculate the corresponding BET areas. This round-robin exercise resulted in a wide range of values. Here, the reproducibility of BET area determination from identical isotherms is demonstrated to be a largely ignored issue, raising critical concerns over the reliability of reported BET areas. To solve this major issue, a new computational approach to accurately and systematically determine the BET area of nanoporous materials is developed. The software, called "BET surface identification" (BETSI), expands on the well-known Rouquerol criteria and makes an unambiguous BET area assignment possible.

Hierarchical Catalysts Prepared by Interzeolite Transformation

Interzeolite transformation has been used to produce a novel family of hierarchical catalysts featuring excellent textural properties, strong acidity, and superior catalytic performance for the Friedel-Crafts alkylation of indole with benzhydrol, the Claisen-Schmidt condensation of benzaldehyde and hydroxyacetophenone, and the cracking of polystyrene. Intermediate solids of the FAU interzeolite transformation into BEA display both increased accessibility─due to the development of mesoporosity─and strong acidity─caused by the presence of ultrasmall crystals or zeolitic fragments in their structure. The use of surfactants allows for the development of the hierarchical catalysts with very narrow pore size distribution. The properties of interzeolite transformation intermediates (ITIs) can be fine-tuned simply by stopping the interconversion at different times.

Micelle Formation inside Zeolites: A Critical Step in Zeolite Surfactant-Templating Observed by Raman Microspectroscopy

Micelle formation inside faujasite (FAU) zeolite, a critical step in the introduction of mesoporosity in zeolites by surfactant templating, has been confirmed by both ¹³C NMR and Raman spectroscopy. Here we provide unambiguous evidence of the incorporation of surfactant molecules inside zeolites during the first step of the surfactant-templating process followed by their self-assembly into micelles after hydrothermal treatment. The homogeneous presence of these micelles throughout zeolite crystals has been directly observed by Raman microspectroscopy, confirming the uniform incorporation of mesoporosity in zeolites by surfactant templating.

Analysis of penitentiary, social and legal operators’ perceptions of prison inmates with intellectual disabilities

Objective

To analyze the different perceptions of professionals about the problem of intellectual disability in the prison setting.

Material and method

Exploratory-descriptive type. In-depth interviews with legal, social and prison operators of Centro Penitenciario de Zuera (Zaragoza).

Results

The narratives of the interviewed subjects point to the aggravating circumstances that a closed social environment can entail for inmates with intellectual disabilities. Communications in the prison administration are written in a technical language that is not understandable for inmates with intellectual deficits.

Discusion

There is a need to give more visibility to the case of inmates with intellectual disabilities. Procedures also need to be applied that favour greater cognitive accessibility for this profile of inmates, along with the promotion of awareness raising and training for professionals to enable them to deal with this issue.

Standing on the Shoulders of Giants - Your Mentors and Role Models Will Shape Your Career

Choosing the right mentors and role models has a profound impact in both our lives and professional careers; however, most often, not enough time or thought is given to this important decision. Because of that, we may miss some great opportunities and limit the potential benefits. In this invited contribution, I share my personal experience on nurturing the relationship with mentors and on choosing role models with my same values and a strong sense of service.

Significance of a polymerase chain reaction method in the detection of Clostridioides difficile

OBJECTIVE

Clostridioides difficile (CD) is the most common cause of nosocomial diarrhea. Detection of CD toxin in patients' faecal samples is the traditional rapid method for the diagnosis of CD infection. Various testing algorithms have been proposed: an initial screening test using a rapid test, and a confirmatory test (cytotoxicity neutralization assay, toxigenic culture, nucleic acid amplification test) for discordant results. The aim of this study was to evaluate the effectiveness of a two-step algorithm using an immunochromatographic test followed of a polymerase chain reaction (PCR).

METHODS

The specimens have been tested according to the following schedule: 1) Step one: All samples were tested for detection of glutamate dehydrogenase antigen (GDH) and toxin A/B using the C. diff QUIK CHEK Complete test. All GDH and toxins positive results were considered CD positives; 2) Step two: When the results were discrepant (only GDH+ or toxins+), the samples were confirmed using the PCR test BD MAX Cdiff. All PCR positive results were considered CD positives.

RESULTS

A total of 2,138 specimens were initially tested. 139 were positive for GDH and toxins. 160 discrepant results (148 GDH+ and 12 toxins+) were tested by PCR, 117 were positive (107/148 GDH+ and 10/12 toxins+).

CONCLUSIONS

The implementation of a PCR method showed an increase de 117 positive results (73.1% of discrepant). Considering the sensitivity of C.diff QUIK CHEK (instructions of manufacturer), the GDH discrepant results may be false negatives, y the samples PCR and toxins positives may be real positives results.

Surfactant-templated zeolites for the production of active pharmaceutical intermediates

A hierarchical USY zeolite has been produced using the surfactant-templating method and used as a catalyst for the production of two important active pharmaceutical ingredients. The presence of intracrystalline mesoporosity in the zeolite results in a significant increase in both the activity (up to 30 fold increase in TOF) and reusability for Friedel-Crafts alkylation and aldol condensation steps.

Thermochemistry of Surfactant-Templating of USY Zeolite

With the aim of understanding the thermochemistry of the introduction of mesoporosity in zeolites by using surfactants, high temperature oxide melt solution calorimetry was used to determine the change in the enthalpy of formation of USY zeolite before and after the introduction of mesoporosity. Our results confirm that this process only slightly destabilizes the zeolite by the additional surface area. However, this can be overcome by the stabilizing effect of the interactions between the surfactant and the zeolite framework.

The Energetics of Surfactant-Templating of Zeolites

Mesoporosity can be conveniently introduced into zeolites by treating them in basic surfactant solutions. The apparent activation energy involved in the formation of mesopores in USY by surfactant-templating was determined using a combination of in situ synchrotron X-ray diffraction and ex situ gas adsorption. Additionally, techniques such as pH measurement and thermogravimetry/differential thermal analysis were employed to determine OH^- evolution and cetyltrimethylammonium ion (CTA⁺ ) uptake during the development of mesoporosity, thereby providing information about the different steps involved. The combination of both in situ and ex situ techniques has allowed determination of the apparent activation energies of the different processes involved in the mesostructuring of USY zeolites for the first time. Apparent activation energies are of the same order of magnitude (30-65 kJ mol^-1 ) as those involved in the crystallization of zeolites. Hence, important mechanistic insight into the surfactant-templating method was obtained.

Visible-Light-Activated Black Organotitanias: How Synthetic Conditions Influence Their Structure and Photocatalytic Activity

A series of low-temperature, visible-light-activated black organotitanias were synthesised through a sol-gel strategy that allowed the in situ incorporation of p-phenylenediamine (PPD) into the framework of anatase nanoparticles. The effect of the synthetic conditions on the crystalline structure and photocatalytic activity of these materials was assessed by several characterisation techniques, which revealed a small crystalline domain size (4.6-5.5 nm), effective incorporation of PPD inside the nanoparticles, and a significant reduction in the band gap of these materials (from 3.2 to 2.7-2.9 eV). A systematic study of the synthetic parameters also allowed a significant reduction of the solvent used for the preparation of these black organotitanias (20-fold), as well as the crystallisation time, without compromising the structural properties and photocatalytic activity of these materials. The organotitanias with the highest PPD content and high crystallinity result in the best performing materials in the photocatalytic degradation of rhodamine 6G under both UV- and visible-light irradiation.

Recent advances in the textural characterization of hierarchically structured nanoporous materials

This review focuses on important aspects of applying physisorption for the pore structural characterization of hierarchical materials such as mesoporous zeolites.

Interleukin-2 as a marker for detecting asymptomatic individuals in areas where Leishmania infantum is endemic

No field method exists for identifying asymptomatic individuals in areas where Leishmania infantum is endemic. This work reports that, 24 h after stimulating whole blood with soluble Leishmania antigen (SLA), plasma interferon-γ (IFN-γ) and interleukin-2 (IL-2) become significantly elevated in samples from asymptomatic individuals (n=47) compared with those from negative controls (n=50), all of them recruited from a blood bank. When compared with the reference test SLA-lymphoproliferative assay, IL-2 appears as a new, 100% sensitive and specific marker for asymptomatic individuals with a positive cellular response (compared with 100% and 84.78%, respectively, for IFN-γ). Further studies in other transmission areas and in other cohorts of exposed people need to be performed to confirm these results. Once validated, IFN-γ and IL-2 levels in SLA-stimulated whole blood could be reliably used in the field to estimate the prevalence of those asymptomatic individuals with Leishmania-specific cellular immune responses.

How to name new chemical elements (IUPAC Recommendations 2016)

A procedure is proposed to name new chemical elements. After the discovery of a new element is established by the joint IUPAC-IUPAP Working Group, the discoverers are invited to propose a name and a symbol to the IUPAC Inorganic Chemistry Division. Elements can be named after a mythological concept, a mineral, a place or country, a property or a scientist. After examination and acceptance by the Inorganic Chemistry Division, the proposal follows the accepted IUPAC procedure and is then ratified by the Council of IUPAC. This document is a slightly amended version of the 2002 IUPAC Recommendations; the most important change is that the names of all new elements should have an ending that reflects and maintains historical and chemical consistency. This would be in general “-ium” for elements belonging to groups 1–16, i.e. including the f-block elements, “-ine” for elements of group 17 and “-on” for elements of group 18.

Rpb1 foot mutations demonstrate a major role of Rpb4 in mRNA stability during stress situations in yeast

The RPB1 mutants in the foot region of RNA polymerase II affect the assembly of the complex by altering the correct association of both the Rpb6 and the Rpb4/7 dimer. Assembly defects alter both transcriptional activity as well as the amount of enzyme associated with genes. Here, we show that the global transcriptional analysis of foot mutants reveals the activation of an environmental stress response (ESR), which occurs at a permissive temperature under optimal growth conditions. Our data indicate that the ESR that occurs in foot mutants depends mostly on a global post-transcriptional regulation mechanism which, in turn, depends on Rpb4-mRNA imprinting. Under optimal growth conditions, we propose that Rpb4 serves as a key to globally modulate mRNA stability as well as to coordinate transcription and decay. Overall, our results imply that post-transcriptional regulation plays a major role in controlling the ESR at both the transcription and mRNA decay levels.

Titania-Silica Materials for Enhanced Photocatalysis

Mesoporous titania-organosilica nanoparticles comprised of anatase nanocrystals crosslinked with organosilica moieties have been prepared by direct co-condensation of a titania precursor, tetrabuthylortotitanate (TBOT), with two organosilica precursors, 1,4-bis(triethoxysilyl) benzene (BTEB) and 1,2-bis(triethoxysilyl) ethane (BTEE), in mild conditions and in the absence of surfactant. These hybrid materials show both high surface areas (200-360 m(2)  g(-1) ) and pore volumes (0.3 cm(3)  g(-1) ) even after calcination, and excellent photoactivity in the degradation of rhodamine 6G and in the partial oxidation of propene under UV irradiation, especially after the calcination of the samples. During calcination, there is a change in the Ti(IV) coordination and an increase in the content of SiOTi moieties in comparison with the uncalcined materials, which seems to be responsible for the enhanced photocatalytic activity of hybrid titania-silica materials as compared to both uncalcined samples and the control TiO2 .

Mesoporous materials for clean energy technologies

Alternative energy technologies are greatly hindered by significant limitations in materials science. From low activity to poor stability, and from mineral scarcity to high cost, the current materials are not able to cope with the significant challenges of clean energy technologies. However, recent advances in the preparation of nanomaterials, porous solids, and nanostructured solids are providing hope in the race for a better, cleaner energy production. The present contribution critically reviews the development and role of mesoporosity in a wide range of technologies, as this provides for critical improvements in accessibility, the dispersion of the active phase and a higher surface area. Relevant examples of the development of mesoporosity by a wide range of techniques are provided, including the preparation of hierarchical structures with pore systems in different scale ranges. Mesoporosity plays a significant role in catalysis, especially in the most challenging processes where bulky molecules, like those obtained from biomass or highly unreactive species, such as CO2 should be transformed into most valuable products. Furthermore, mesoporous materials also play a significant role as electrodes in fuel and solar cells and in thermoelectric devices, technologies which are benefiting from improved accessibility and a better dispersion of materials with controlled porosity.

Atypical presentation in adults in the largest community outbreak of leishmaniasis in Europe (Fuenlabrada, Spain)

Since 2009, the largest reported outbreak of leishmaniasis by Leishmania infantum in Europe was reported in Fuenlabrada, Spain. In our hospital, 90 adults with localized leishmanial lymphadenopathy (LLL) or visceral leishmaniasis (VL) were treated during this outbreak; 72% were men, and the mean age was 46.2 years (range 15-95 years). A total of 17 cases (19%) were LLL, an atypical form with isolated lymphadenopathies without other symptoms. All LLL cases occurred in immunocompetent subjects, and only one subject (6%) was a native of sub-Saharan Africa. Diagnosis was performed by fine needle aspiration cytology of the lymphadenopathy. Serology was negative in 38%. LLL outcomes at 6 months were benign, even with doses of liposomal amphotericin B that were often lower (10 mg/kg) than those recommended for VL in Mediterranean areas. A total of 73 subjects (81%) presented with typical VL; 66% of this group were immunocompetent, and 50% of those who were immunocompetent were descendants of natives of sub-Saharan Africa. The rK39 test and polymerase chain reaction were the most useful tests for confirmation of the diagnosis. An initial response to treatment was observed in 99% of cases, and relapses occurred in 14% of cases. Leishmaniasis should be included in the differential diagnosis of isolated lymphadenopathies in endemic areas. LLL could be considered a more benign entity, one different than VL, and less aggressive management should be studied in future investigations.

Diversity of CRISPR loci in Escherichia coli

CRISPR (clustered regularly interspaced short palindromic repeats) and CAS (CRISPR-associated sequence) proteins are constituents of a novel genetic barrier that limits horizontal gene transfer in prokaryotes by means of an uncharacterized mechanism. The fundamental discovery of small RNAs as the guides of the defence apparatus arose as a result of Escherichia coli studies. However, a survey of the system diversity in this species in order to further contribute to the understanding of the CRISPR mode of action has not yet been performed. Here we describe two CRISPR/CAS systems found in E. coli, following the analysis of 100 strains representative of the species' diversity. Our results substantiate different levels of activity between loci of both CRISPR types, as well as different target preferences and CRISPR relevances for particular groups of strains. Interestingly, the data suggest that the degeneration of one CRISPR/CAS system in E. coli ancestors could have been brought about by self-interference.

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated CRISPR-associated sequence (CAS) proteins constitute a novel antiviral defence system that is widespread in prokaryotes. Repeats are separated by spacers, some of them homologous to sequences in mobile genetic elements. Although the whole process involved remains uncharacterized, it is known that new spacers are incorporated into CRISPR loci of the host during a phage challenge, conferring specific resistance against the virus. Moreover, it has been demonstrated that such interference is based on small RNAs carrying a spacer. These RNAs would guide the defence apparatus to foreign molecules carrying sequences that match the spacers. Despite this essential role, the spacer uptake mechanism has not been addressed. A first step forward came from the detection of motifs associated with spacer precursors (proto-spacers) of Streptococcus thermophilus, revealing a specific recognition of donor sequences in this species. Here we show that the conservation of proto-spacer adjacent motifs (PAMs) is a common theme for the most diverse CRISPR systems. The PAM sequence depends on the CRISPR-CAS variant, implying that there is a CRISPR-type-specific (motif-directed) choice of the spacers, which subsequently determines the interference target. PAMs also direct the orientation of spacers in the repeat arrays. Remarkably, observations based on such polarity argue against a recognition of the spacer precursors on transcript RNA molecules as a general rule.

Viral monitoring and successful treatment of a ganciclovir-resistant cytomegalovirus infection in a heart transplant recipient

We reported a ganciclovir (GCV)-resistant cytomegalovirus (CMV) infection in a heart transplant recipient. Genotypic and phenotypic susceptibility assays demonstrated an A594V mutation in the UL97 phosphotransferase gene and GCV IC(50)>96 microM. Low GCV concentration exposure, immunosuppressive treatment, donor-positive/recipient-negative CMV serostatus, viral reactivations within antiviral prophylaxis or treatment, contributed to GCV-resistant strain selection.

Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation

Genome-wide analysis of the wine yeast strain Saccharomyces cerevisiae PYCC4072 identified 36 genes highly expressed under conditions of low or absent nitrogen in comparison with a nitrogen-replete condition. Reverse transcription-PCR analysis for four of these transcripts with this strain and its validation with another wine yeast strain underlines the usefulness of these signature genes for predicting nitrogen deficiency and therefore the diagnosis of wine stuck/sluggish fermentations.

Evolution of the antimicrobial resistance of Pseudomonas aeruginosa in Spain: second national study (2003)

The second national prevalence study of Pseudomonas aeruginosa has been carried out in Spain. A total of 1250 clinical isolates of P. aeruginosa were collected from 127 hospitals in 1 week in 2003 and the resistance data gathered from the isolates was compared with those of the first study in 1998 (1014 isolates from 136 hospitals). Antimicrobial susceptibility testing was performed in both studies in the same laboratory. The most active antimicrobials were piperacillin, piperacillin-tazobactam, and amikacin (< or =10% resistant) and resistance to these antimicrobials did not change over the time. The least active were ofloxacin and gentamicin (> or =30% resistant). From 1998 to 2003, resistance increased significantly to ciprofloxacin (23% vs. 28%, respectively, p=0.015); ofloxacin (30% vs. 37%, p=0.002); imipenem (14% vs. 18%, p=0.017) and meropenem (8% vs. 13%, p <0.001). Resistance to aztreonam (23%), ceftazidime (16%), cefepime (20%), ticarcillin (13%) and tobramycin (11%) remained stable. Isolates from inpatients were significantly more resistant than those from outpatients to all antimicrobials, with the exception of fluoroquinolones and aminoglycosides (p <0.01). Isolates from outpatients were significantly more resistant to these two groups (p <0.05) than to other antimicrobials. In Spain, from 1998 to 2003, the susceptibility pattern of P. aeruginosa to antimicrobial agents has changed. Isolates have become significantly more resistant to fluoroquinolones and carbapenems. However, resistance to beta-lactams and aminoglycosides remains stable.

Ultrasonic tissue characterization for monitoring nanostructured TiO2-induced bone growth

The use of bioactive nanostructured TiO2 has recently been proposed for improving orthopaedic implant adhesion due to its improved biocompatibility with bone, since it induces: (i) osteoblast function, (ii) apatite nucleation and (iii) protein adsorption. The present work focuses on a non-ionizing radiation emitting technique for quantifying in real time the improvement in terms of mechanical properties of the surrounding bone due to the presence of the nanostructured TiO2 prepared by controlled precipitation and acid ageing. The mechanical strength is the ultimate goal of a bone implant and is directly related to the elastic moduli. Ultrasonics are high frequency mechanical waves and are therefore suited for characterizing elastic moduli. As opposed to echographic techniques, which are not correlated to elastic properties and are not able to penetrate bone, a low frequency ultrasonic transmission test is proposed, in which a P-wave is transmitted through the specimen and recorded. The problem is posed as an inverse problem, in which the unknown is a set of parameters that describe the mechanical constants of the sequence of layers. A finite element numerical model that depends on these parameters is used to predict the transformation of the waveform and compare to the measurement. The parameters that best describe the real tissue are obtained by minimizing the discrepancy between the real and numerically predicted waveforms. A sensitivity study to the uncertainties of the model is performed for establishing the feasibility of using this technique to investigate the macroscopic effect on bone growth of nanostructured TiO2 and its beneficial effect on implant adhesion.

Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation

Gene expression profiles of a wine strain of Saccharomyces cerevisiae PYCC4072 were monitored during alcoholic fermentations with three different nitrogen supplies: (i) control fermentation (with enough nitrogen to complete sugar fermentation), (ii) nitrogen-limiting fermentation, and (iii) the addition of nitrogen to the nitrogen-limiting fermentation (refed fermentation). Approximately 70% of the yeast transcriptome was altered in at least one of the fermentation stages studied, revealing the continuous adjustment of yeast cells to stressful conditions. Nitrogen concentration had a decisive effect on gene expression during fermentation. The largest changes in transcription profiles were observed when the early time points of the N-limiting and control fermentations were compared. Despite the high levels of glucose present in the media, the early responses of yeast cells to low nitrogen were characterized by the induction of genes involved in oxidative glucose metabolism, including a significant number of mitochondrial associated genes resembling the yeast cell response to glucose starvation. As the N-limiting fermentation progressed, a general downregulation of genes associated with catabolism was observed. Surprisingly, genes encoding ribosomal proteins and involved in ribosome biogenesis showed a slight increase during N starvation; besides, genes that comprise the RiBi regulon behaved distinctively under the different experimental conditions. Here, for the first time, the global response of nitrogen-depleted cells to nitrogen addition under enological conditions is described. An important gene expression reprogramming occurred after nitrogen addition; this reprogramming affected genes involved in glycolysis, thiamine metabolism, and energy pathways, which enabled the yeast strain to overcome the previous nitrogen starvation stress and restart alcoholic fermentation.

CYGD: the Comprehensive Yeast Genome Database

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.

Pilot randomized study of early tacrolimus withdrawal from a regimen with sirolimus plus tacrolimus in kidney transplantation

We performed a randomized trial to compare two regimens of low-risk kidney allograft recipients in the first year after transplantation. Both regimens initially included sirolimus, tacrolimus and steroids; one with long-term maintenance with these drugs vs. tacrolimus withdrawal. Group I: sirolimus levels of 4-8 ng/mL, plus tacrolimus 8-12 ng/mL for 3 months, and 5-10 ng/mL after month 3. Group II: sirolimus concentration of 8-16 ng/mL, plus tacrolimus 3-8 ng/mL with tacrolimus elimination from month 3 onwards. Owing to difficulties in achieving target levels, the protocol was amended to increase the doses. Eighty-seven patients were recruited. In the intention-to-treat analysis, glomerular filtration rate (GFR) at 12 months, adjusted to zero for graft loss, was similar in both groups (58.8 and 59.9 mL/min). Analysis of patients remaining on protocol showed that GFR was higher in group II only in the patients postamendment (58.4 and 72.9 mL/min, p = 0.03). Rates of biopsy-confirmed rejection (BCAR) were 9.3% and 22.7% in groups I and II, respectively (p = NS). After amendment, BCAR rates were 10.3% and 11.1% (p = NS). Diastolic blood pressure was significantly lower in patients who eliminated tacrolimus (80.4 vs. 75.6 mmHg) (p = 0.03). Combining sirolimus and tacrolimus with adequate loading doses was associated with a low incidence of BCAR, and allowed tacrolimus elimination in a high proportion of patients, which may be followed by amelioration in renal function and blood pressure.

Application of molecular biology techniques to the diagnosis of nontuberculous mycobacterial infections

A total of 19,723 clinical samples were cultivated for the detection of mycobacteria from January 1995 to March 2001. The 203 strains of nontuberculous mycobacteria isolated were identified with the use of molecular techniques in combination with traditional biochemical tests. The molecular methods applied were PCR-restriction fragment length polymorphism analysis (PRA) alone or in combination with 16S rRNA and 16S-23S spacer sequencing. The patient records of those with specimens positive for mycobacteria were analysed to evaluate the clinical significance of the culture results. Twenty-five of the 124 patients analysed (20%) were regarded as having clinical mycobacteriosis. The main species associated with mycobacteriosis were: Mycobacterium avium (13 cases), M. intracellulare (2 cases), M. kansasii (5 cases), M. chelonae (2 cases), M. malmoense (1 case), M. scrofulaceum (1 case) and M. marinum (1 case). The use of PRA alone or in combination with gene sequencing provided valuable help in discerning mycobacteria at both the intra- and interspecies level, thus contributing to a faster and more efficient diagnosis and epidemiological follow-up.

RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions

A novel database, under the acronym RISSC (Ribosomal Intergenic Spacer Sequence Collection), has been created. It compiles more than 1600 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and is accessible through the Internet (http://ulises.umh.es/RISSC), where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches. Additionally, a characteristic feature of this region, the presence/absence and nature of tRNA genes within the spacer, is included in all the entries, even when not previously indicated in the original database. All these combined features could provide a useful documentation tool for studies on evolution, identification, typing and strain characterization, among others.

Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I

The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.