The use of readily available laboratory tests for the identification of the emerging yeast Candida auris in Mexico.

Identification of the emerging multidrug-resistant yeast Candida auris is challenging. Here, we describe the role of the Mexico national reference laboratory Instituto de Diagnóstico y Referencia Epidemiológicos Dr. Manuel Martínez Báez (InDRE) and the Mexican national laboratory network in the identification of C. auris. Reference identification of six suspected isolates was done based on phenotypic and molecular laboratory methods, including growth in special media, evaluation of isolate micromorphology, and species-specific PCR and pan-fungal PCR and sequencing. The four C. auris isolates identified were able to grow on modified Sabouraud agar with 10% NaCl incubated at 42 °C. With one exception, isolates of C. auris were spherical to ovoid yeast-like cells and blastoconidia, with no hyphae or pseudohyphae on cornmeal agar. C. auris isolates were resistant to fluconazole. Species-specific and pan-fungal PCR confirmed isolates as C. auris. Sequence analysis revealed the presence of two different C. auris clades in Mexico, clade I (South Asia) and clade IV (South America).

Unraveling the Fungal Community Associated with Leaf Spot on Crataegus sp.

Crataegus sp. is a tree that grows in temperate zones with worldwide distribution and is commonly known in Mexico as tejocote. The use of products derived from Crataegus in traditional medicine, food, and cosmetics has increased over the last few years and the relevance of this plant has also grown. Here, we report a disease that was observed in tejocote plants that grew both in the wild and in greenhouses in Puebla (Mexico). The disease was characterized by necrotic spots on the leaf ranging from brown to reddish tones that were accompanied by structures on the back of the leaf. Furthermore, we investigated the fungal genera associated with infected leaves in wild tejocote plants, from which we recovered Alternaria sp., Aureobasidium sp., Dreschlera sp., Fusarium sp., Paecilomyces sp. and Ulocladium sp. genera. Inoculation on healthy Crataegus sp. plants with isolate UAP140 showed similar symptoms as observed in nature, while inoculation with UAP127 resulted in the development of necrotic lesions in the leaf. The identity of these isolates was further studied through the phylogenetic analysis of the ribosomal DNA internal transcribed spacer (ITS) region, where isolate UAP140 showed the highest identity with Fusarium equiseti and isolate UAP127 was similar to Alternaria arborescens. To our knowledge, this is the first report of a characteristic disease developed in Crataegus sp. plants in Mexico where the fungal community associated to the lesion was analyzed. Further studies would be necessary to determine the ecological and environmental implications of the microbiome on the appearance and development of the disease.

Emerging Drugs for the Treatment of Breast Cancer Brain Metastasis: A Review of Patent Literature.

BACKGROUND: Despite dramatic advances in cancer treatment that lead to long-term survival, there is an increasing number of patients presenting with clinical manifestations of cerebral metastasis in breast cancer, for whom only palliative treatment options exist. OBJECTIVE: The present review based on researches aims to provide identification of recent patens of breast cancer brain metastasis that may have application in improving cancer treatment. METHODS: Recent patents regarding the breast cancer brain metastasis were obtained from USPTO patent databases, Esp@cenet, Patentscope and Patent Inspiration®. RESULTS: A total of 55 patent documents and 35 drug targets were recovered. Of these, a total of 45 patents and 10 patents were biotech drugs and chemical drugs, respectively. Among the target drugs analyzed were neurotrophin-3, protocadherin 7, CXCR4, PTEN, GABA receptor 3, L1CAM, PI3K-Akt / mTOR, VEGFR2, Claudin-5, Occludin, and NKG2A, among others. CONCLUSION: In this study, we found 35 drug targets for metastasis to the brain in breast cancer, with 60% of them including only one patent, which establishes that this area of research is very recent, and that these targets have recently been linked to metastasis to the brain. On the other hand, 19 drug targets, among them VEGF, VEGFR2, CXCL12, and CXCR4, have been addressed for the first time until 6 years ago, confirming that the development of drugs for brain metastasis in breast cancer is an incipient area, but with interesting potential. Interestingly, the stage of inside the brain, was the stage with the lowest amount of drug targets, which places it as a priority for research and drug development.

Fungal Diversity and Community Composition of Culturable Fungi in Stanhopea trigrina Cast Gibberellin Producers.

Stanhopea tigrina is a Mexican endemic orchid reported as a threatened species. The naturally occurring microorganisms present in S. tigrina are unknown. In this work, we analyzed the diversity of endophytic and epiphytic culturable fungi in S. tigrina according to morphological and molecular identification. Using this combined approach, in this study we retrieved a total of 634 fungal isolates that presented filamentous growth, which were grouped in 134 morphotypes that were associated to 63 genera, showing that S. tigrina harbors a rich diversity of both endophytic and epiphytic fungi. Among these, the majority of the isolates corresponded to Ascomycetes, with Trichoderma and Penicillium as the most frequent genera followed by Fusarium and Aspergillus. Non-ascomycetes isolated were associated only to the genus Mucor (Mucoromycota) and Schizophyllum (Basidiomycota). Identified genera showed a differential distribution considering their epiphytic or endophytic origin, the tissue from which they were isolated, and the ability of the orchid to grow on different substrates. To our knowledge, this work constitutes the first study of the mycobiome of S. tigrina. Interestingly, 21 fungal isolates showed the ability to produce gibberellins. Almost half of the isolates were related to the gibberellin-producer genus Penicillium based on morphological and molecular identification. However, the rest of the isolates were related to the following genera, which have not been reported as gibberellin producers so far: Bionectria, Macrophoma, Nectria, Neopestalotiopsis, Talaromyces, Trichoderma, and Diplodia. Taken together, we found that S. tigrina possess a significant fungal diversity that could be a rich source of fungal metabolites with the potential to develop biotechnological approaches oriented to revert the threatened state of this orchid in the near future.

Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria.

Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.

Alternative Splicing as a Target for Cancer Treatment.

Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.

Alternative Splicing in Breast Cancer and the Potential Development of Therapeutic Tools.

Alternative splicing is a key molecular mechanism now considered as a hallmark of cancer that has been associated with the expression of distinct isoforms during the onset and progression of the disease. The leading cause of cancer-related deaths in women worldwide is breast cancer, and even when the role of alternative splicing in this type of cancer has been established, the function of this mechanism in breast cancer biology is not completely decoded. In order to gain a comprehensive view of the role of alternative splicing in breast cancer biology and development, we summarize here recent findings regarding alternative splicing events that have been well documented for breast cancer evolution, considering its prognostic and therapeutic value. Moreover, we analyze how the response to endocrine and chemical therapies could be affected due to alternative splicing and differential expression of variant isoforms. With all this knowledge, it becomes clear that targeting alternative splicing represents an innovative approach for breast cancer therapeutics and the information derived from current studies could guide clinical decisions with a direct impact in the clinical advances for breast cancer patients nowadays.

Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment.

In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics.

In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis.

The molecular mechanisms regulating the accuracy of gene expression are still not fully understood. Among these mechanisms, Nonsense-mediated Decay (NMD) is a quality control process that detects post-transcriptionally abnormal transcripts and leads them to degradation. The UPF1 protein lays at the heart of NMD as shown by several structural and functional features reported for this factor mainly for Homo sapiens and Saccharomyces cerevisiae. This process is highly conserved in eukaryotes but functional diversity can be observed in various species. Ustilago maydis is a basidiomycete and the best-known smut, which has become a model to study molecular and cellular eukaryotic mechanisms. In this study, we performed in silico analysis to investigate the structural and biochemical properties of the putative UPF1 homolog in Ustilago maydis. The putative homolog for UPF1 was recognized in the annotated genome for the basidiomycete, exhibiting 66% identity with its human counterpart at the protein level. The known structural and functional domains characteristic of UPF1 homologs were also found. Based on the crystal structures available for UPF1, we constructed different three-dimensional models for umUPF1 in order to analyze the secondary and tertiary structural features of this factor. Using these models, we studied the spatial arrangement of umUPF1 and its capability to interact with UPF2. Moreover, we identified the critical amino acids that mediate the interaction of umUPF1 with UPF2, ATP, RNA and with UPF1 itself. Mutating these amino acids in silico showed an important effect over the native structure. Finally, we performed molecular dynamic simulations for UPF1 proteins from H. sapiens and U. maydis and the results obtained show a similar behavior and physicochemical properties for the protein in both organisms. Overall, our results indicate that the putative UPF1 identified in U. maydis shows a very similar sequence, structural organization, mechanical stability, physicochemical properties and spatial organization in comparison to the NMD factor depicted for Homo sapiens. These observations strongly support the notion that human and fungal UPF1 could perform equivalent biological activities.

The decrease in the population of Gluconacetobacter diazotrophicus in sugarcane after nitrogen fertilization is related to plant physiology in split root experiments.

It has been established that a decrease in the population of Gluconacetobacter diazotrophicus associated with sugarcane occurs after nitrogen fertilization. This fact could be due to a direct influence of NH(4)NO(3) on bacterial cells or to changes in plant physiology after fertilizer addition, affecting bacterial establishment. In this work, we observed that survival of G. diazotrophicus was directly influenced when 44.8mM of NH(4)NO(3) (640mgN/plant) was used for in vitro experiments. Furthermore, micropropagated sugarcane plantlets were inoculated with G. diazotrophicus and used for split root experiments, in which both ends of the system were fertilized with a basal level of NH(4)NO(3) (0.35mM; 10mgN/plant). Twenty days post inoculation (dpi) one half of the plants were fertilized with a high dose of NH(4)NO(3) (6.3mM; 180 mgN/plant) on one end of the system. This nitrogen level was lower than that directly affecting G. diazotrophicus cells; however, it caused a decrease in the bacterial population in comparison with control plants fertilized with basal nitrogen levels. The decrease in the population of G. diazotrophicus was higher in pots fertilized with a basal nitrogen level when compared with the corresponding end supplied with high levels of NH4NO3 (100dpi; 80 days post fertilization) of the same plant system. These observations suggest that the high nitrogen level added to the plants induce systemic physiological changes that affect the establishment of G. diazotrophicus.

La disminución de la población de Gluconacetobacter diazotrophicus en caña de azúcar, después de la fertilización nitrogenada, está relacionada con la fisiología de las plantas en experimentos de raíz dividida / The decrease in the population of Gluconacetobacter diazotrophicus in sugarcane after nitrogen fertilization is related to plant physiology in split root experiments

It has been established that a decrease in the population of Gluconacetobacter diazotrophicus associated with sugarcane occurs after nitrogen fertilization. This fact could be due to a direct influence of NH4NO3 on bacterial cells or to changes in plant physiology after fertilizer addition, affecting bacterial establishment. In this work, we observed that survival of G. diazotrophicus was directly influenced when 44.8 mM of NH4NO3 (640 mg N/plant) was used for in vitro experiments. Furthermore, micropropagated sugarcane plantlets were inoculated with G. diazotrophicus and used for split root experiments, in which both ends of the system were fertilized with a basal level of NH4NO3 (0.35 mM; 10 mg N/plant). Twenty days post inoculation (dpi) one half of the plants were fertilized with a high dose of NH4NO3 (6.3 mM; 180 mg N/plant) on one end of the system. This nitrogen level was lower than that directly affecting G. diazotrophicus cells; however, it caused a decrease in the bacterial population in comparison with control plants fertilized with basal nitrogen levels. The decrease in the population of G. diazotrophicus was higher in pots fertilized with a basal nitrogen level when compared with the corresponding end supplied with high levels of NH4NO3 (100 dpi; 80 days post fertilization) of the same plant system. These observations suggest that the high nitrogen level added to the plants induce systemic physiological changes that affect the establishment of G. diazotrophicus.

La población de Gluconacetobacter diazotrophicus asociada a la caña de azúcar disminuye después de la fertilización nitrogenada, lo cual podría ocurrir por la influencia directa del NH4NO3 sobre la supervivencia bacteriana, o por cambios en la fisiología de las plantas, que impiden el establecimiento bacteriano. En el presente trabajo se observó que en experimentos in vitro la supervivencia de G. diazotrophicus fue influenciada por 44,8 mM de NH4NO3 (640 mg N/plant). Además, G. diazotrophicus fue inoculado en plántulas micropropagadas de caña de azúcar, que fueron usadas para realizar experimentos de raíz dividida, en las que ambos extremos de los sistemas se fertilizaron con un nivel basal de NH4NO3 (0,35 mM; 10 mg N/planta). A los 20 días posteriores a la inoculación (dpi), la mitad de plantas fueron fertilizadas en uno de sus extremos con una dosis elevada de NH4NO3 (6,3 mM; 180 mg of N/plant). Este nivel fue menor al que afectó directamente a las células de G. diazotrophicus; sin embargo, provocó una disminución de la población bacteriana en comparación con plantas testigo fertilizadas con niveles basales de nitrógeno. La disminución de la población fue mayor para raíces fertilizadas con un nivel basal de nitrógeno en comparación con las raíces fertilizadas con altos niveles del mismo sistema de plantas (100 dpi; 80 días posfertilización). Estas observaciones indican que el alto nivel de nitrógeno añadido a las plantas inducen cambios fisiológicos sistémicos que afectan el establecimiento de G. diazotrophicus.

Regulación del splicing alternativo: Implicaciones en el diagnóstico y tratamiento del cáncer / Alternative splicing regulation: Implications in cancer diagnosis and treatment

La expresión de la información genética es regulada por procesos como el splicing del ARN mensajero, mecanismo propuesto por Phil Sharp y Richard Roberts, quienes demostraron la existencia de secuencias intrónicas, las cuales interrumpen a la mayoría de los genes estructurales en eucariotes y deben ser removidas con gran precisión. Dicha remoción de intrones se denomina splicing, y permite generar variantes proteicas a partir de un solo gen, cada una con funciones diversas y, a menudo, antagónicas. Actualmente se sabe que el splicing es la principal fuente de diversidad proteica, ya que el 70% de los genes humanos lo sufren, y defectos en este proceso originan hasta el 50% de las enfermedades genéticas, incluido el cáncer. Cuando estos defectos se presentan en genes involucrados en adhesión, proliferación y ciclo celular, repercuten en la progresión de procesos cancerosos cuyo diagnóstico, tratamiento y prognosis puede determinarse en base a su perfil de splicing (AU)

The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called “splicing”, which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile (AU)

[Alternative splicing regulation: implications in cancer diagnosis and treatment]. / Regulación del splicing alternativo: Implicaciones en el diagnóstico y tratamiento del cáncer.

The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called "splicing", which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile.

PTB binds to the 3' untranslated region of the human astrovirus type 8: a possible role in viral replication.

The 3' untranslated region (3'UTR) of human astroviruses (HAstV) consists of two hairpin structures (helix I and II) joined by a linker harboring a conserved PTB/hnRNP1 binding site. The identification and characterization of cellular proteins that interact with the 3'UTR of HAstV-8 virus will help to uncover cellular requirements for viral functions. To this end, mobility shift assays and UV cross-linking were performed with uninfected and HAstV-8-infected cell extracts and HAstV-8 3'UTR probes. Two RNA-protein complexes (CI and CII) were recruited into the 3'UTR. Complex CII formation was compromised with cold homologous RNA, and seven proteins of 35, 40, 45, 50, 52, 57/60 and 75 kDa were cross-linked to the 3'UTR. Supermobility shift assays indicated that PTB/hnRNP1 is part of this complex, and 3'UTR-crosslinked PTB/hnRNP1 was immunoprecipitated from HAstV-8 infected cell-membrane extracts. Also, immunofluorescence analyses revealed that PTB/hnRNP1 is distributed in the nucleus and cytoplasm of uninfected cells, but it is mainly localized perinuclearly in the cytoplasm of HAstV-8 infected cells. Furthermore, the minimal 3'UTR sequences recognized by recombinant PTB are those conforming helix I, and an intact PTB/hnRNP1-binding site. Finally, small interfering RNA-mediated PTB/hnRNP1 silencing reduced synthesis viral genome and virus yield in CaCo2 cells, suggesting that PTB/hnRNP1 is required for HAstV replication. In conclusion, PTB/hnRNP1 binds to the 3'UTR HAstV-8 and is required or participates in viral replication.

Growth response of maize plantlets inoculated with Enterobacter spp., as a model for alternative agriculture.

A maize rhizosphere isolate was phenotypically and genotypically characterized and identified as Enterobacter spp. bacterium. Germinated seeds were inoculated, the plantlets were sown in vermiculite and in soil and grown under laboratory and field conditions, respectively. The adherence, colonization and plant growth promotion capability of Enterobacter sp. UAPS03001 was evaluated in "Rojo-Criollo" maize under laboratory conditions. Twenty days after inoculation, the treated plantlets showed larger biomass than non-inoculated ones. In field grown plants, the kernel biomass was also greater in inoculated than in non-inoculated plants. The inoculation of maize sprouts with plant growth- promoting bacteria before their sowing in the field would be an alternative practice for achieving successful yield in temporal agriculture.

hnRNP proteins and splicing control.

Proteins of the heterogeneous nuclear ribonucleoparticles (hnRNP) family form a structurally diverse group of RNA binding proteins implicated in various functions in metazoans. Here we discuss recent advances supporting a role for these proteins in precursor-messenger RNA (pre-mRNA) splicing. Heterogeneous nuclear RNP proteins can repress splicing by directly antagonizing the recognition of splice sites, or can interfere with the binding of proteins bound to enhancers. Recently, hnRNP proteins have been shown to hinder communication between factors bound to different splice sites. Conversely, several reports have described a positive role for some hnRNP proteins in pre-mRNA splicing. Moreover, cooperative interactions between bound hnRNP proteins may encourage splicing between specific pairs of splice sites while simultaneously hampering other combinations. Thus, hnRNP proteins utilize a variety of strategies to control splice site selection in a manner that is important for both alternative and constitutive pre-mRNA splicing.

Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing.

hnRNP A/B proteins modulate the alternative splicing of several mammalian and viral pre-mRNAs, and are typically viewed as proteins that enforce the activity of splicing silencers. Here we show that intronic hnRNP A/B-binding sites (ABS) can stimulate the in vitro splicing of pre-mRNAs containing artificially enlarged introns. Stimulation of in vitro splicing could also be obtained by providing intronic ABS in trans through the use of antisense oligonucleotides containing a non-hybridizing ABS-carrying tail. ABS-tailed oligonucleotides also improved the in vivo inclusion of an alternative exon flanked by an enlarged intron. Notably, binding sites for hnRNP F/H proteins (FBS) replicate the activity of ABS by improving the splicing of an enlarged intron and by modulating 5' splice-site selection. One hypothesis formulated to explain these effects is that bound hnRNP proteins self-interact to bring in closer proximity the external pair of splice sites. Consistent with this model, positioning FBS or ABS at both ends of an intron was required to stimulate splicing of some pre-mRNAs. In addition, a computational analysis of the configuration of putative FBS and ABS located at the ends of introns supports the view that these motifs have evolved to support cooperative interactions. Our results document a positive role for the hnRNP A/B and hnRNP F/H proteins in generic splicing, and suggest that these proteins may modulate the conformation of mammalian pre-mRNAs.

Two exonic elements in the flanking constitutive exons control the alternative splicing of the alpha exon of the ZO-1 pre-mRNA.

The 240-bp alpha exon of the tight junction (TJ) protein ZO-1 pre-mRNA is alternatively spliced. Expression of both ZO-1alpha+/ZO-1alpha- isoforms results in hermetic TJs, and these become leaky when ZO-1alpha- expression prevails. The alpha exon inclusion/skipping mechanism was studied by in vivo RT-PCR splicing assays in neural and epithelial cells, utilizing a canine minigene construct containing the alpha exon, and the flanking introns and exons. Inclusion of the alpha exon always occurs in wild-type MDCK cells and it is detectable in transfected HeLa cells. However, the alpha exon is skipped in transfected neural cells. Accordingly, both 5' and 3' splice sites surrounding the alpha exon appear to be suboptimal and no cis-acting splicing control elements were found in this exon. Deletion analysis revealed an 83-bp splicing enhancer in the downstream exon and a 35-bp splicing silencer at the beginning of the upstream exon. In epithelial cells all constructs rendered alpha exon inclusion. We conclude that, in neural cells, skipping of the alpha exon depends on two antagonistic exonic elements located in the flanking constitutive exons.