Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response.

Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol productivity requires overcoming several biotechnological challenges due to the cellular inhibition caused by the inhibitors present in the medium. In this work, K. marxianus SLP1 was adapted to increase its tolerance to a mix of inhibitory compounds using the adaptive laboratory evolution strategy to study the adaptation and stress response mechanisms used by this non-Saccharomyces yeast. The fermentative and physiological parameters demonstrated that the adapted K. marxianus P8 had a better response against the synergistic effects of multiple inhibitors because it reduced the lag phase from 12 to 4 h, increasing the biomass by 40% and improving the volumetric ethanol productivity 16-fold than the parental K. marxianus SLP1. To reveal the effect of adaptation process in P8, transcriptome analysis was carried out; the result showed that the basal gene expression in P8 changed, suggesting the biological capability of K. marxianus to activate the adaptative prediction mechanism. Similarly, we carried out physiologic and transcriptome analyses to reveal the mechanisms involved in the stress response triggered by furfural, the most potent inhibitor in K. marxianus. Stress response studies demonstrated that P8 had a better physiologic response than SLP1, since key genes related to furfural transformation (ALD4 and ALD6) and stress response (STL1) were upregulated. Our study demonstrates the rapid adaptability of K. marxianus to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol. KEY POINTS: • K. marxianus was adapted to increase its tolerance to a mix of inhibitory compounds • The basal gene expression of K. marxianus changed after the adaptation process • Adapted K. marxianus showed a better physiological response to stress by inhibitors • Transcriptome analyses revealed key genes involved in the stress response.

Randomized, double-blind, placebo-controlled clinical trial on the usefulness of probiotic Lactobacillus reuteri in bismuth-containing quadruple eradication therapy for infection with Helicobacter pylori.

INTRODUCTION: the primary goal of this study was to compare gastrointestinal symptom reduction in patients on bismuth-containing quadruple eradication therapy supplemented with Lactobacillus reuteri strains (DSM 17938 and ATCC PTA 6475) or placebo. MATERIALS AND METHODS: this was a randomized, double-blind, parallel-arm, placebo-controlled clinical trial. Patients received a first-line eradication regimen based on bismuth subcitrate potassium, metronidazole, tetracycline hydrochloride (three-in-one capsules) and omeprazole 40 mg twice a day for ten days, plus a probiotic or placebo tablet for 30 days. During follow-up, gastrointestinal symptoms were assessed using an evaluation scale (GSRS), and adverse events were collected at 0, 14, 28 and 56 days. RESULTS: a total of 80 patients were included from February 2018 to May 2019 at a single site. Eradication therapy was effective in 85 % of patients, with no differences between treatment arms. In the group receiving the probiotic, abdominal pain decreased in 42 % of patients, compared with 19 % in the control group (OR: 0.27; CI, 0.13-0.58; p < 0.001), and abdominal distension decreased in 25 % versus 17 % in the control group (OR: 0.24; IC, 0.19-0.84; p < 0.001); Conclusions: treatment with L. reuteri only reduced abdominal pain and distension. Further studies are needed to establish the role of probiotics as adjuvant therapy in H. pylori eradication.

An unusual association: median arcuate ligament syndrome and nutcracker syndrome.

We present a case of arcuate ligament syndrome diagnosed in a 23-year-old patient with epigastric pain, vomiting and weight loss, using Doppler ultrasound and CT-angiography, treated by surgical resection of the ligament with complete resolution of symptoms. In addition, incidentally the patient was diagnosed with a nutcracker syndrome, without clinical repercussions.

[Written tests analysis under the principles of authentic assessment. A comparative study of written tests of medical and other undergraduate programs]. / Análisis de pruebas escritas bajo los principios de la evaluación auténtica. Estudio comparativo entre carreras de la salud y otras carreras de dos universidades de la Región del Biobío.

BACKGROUND: Learning assessment has great impact in students' achievement. However, it is one of the least intervened and researched areas in higher education institutions, all over the world. AIM: To compare the written tests applied to students of three health science undergraduate programs (Speech Therapy, Medical Technology and Nursing), with the written tests of three programs of other areas (Business and Administration, Psychology and Bioengineering). MATERIAL AND METHODS: Comparisons were done using the Authentic Assessment Model's indicators. Also, the magnitude of the change in these variables was evaluated in these two groups of undergraduate programs, after the participation of the teachers in a training program based on this model. A quantitative and repeated measurements design was used. Nineteen teachers participated (nine from medical sciences and 10 from other areas), who drafted 88 written tests before the intervention (which involved 1,318 items) and 93 written tests (that grouped 1,051 items) after it. Items were analyzed using a Hierarchical Lineal Model (HLM), controlling the tests' and the teachers' effects. RESULTS: Both groups of undergraduate programs use multiple choice items with a higher frequency, although there were differences in the rest of the items. Also, HLM analysis showed that these programs differed in their changes after the intervention. Health science programs had less improvement in changing the kind of items used, but improved more in Authentic Assessment indicators. CONCLUSIONS: Written tests improved after an intervention aiming to improve the teachers' skills to prepare such tests.

Fetal Magnetic Resonance Imaging Findings in Prenatal Zika Virus Infection.

Brain lesions and malformations have been described on ultrasonography of prenatal Zika infection; however, there are scarce reports about fetal magnetic resonance (MR) findings. We report 3 cases of fetuses with confirmed intrauterine Zika virus infection evaluated by ultrasound and fetal MR. Various morphometric measurements were assessed and brain maturation was calculated with the fetal total maturation score. Fetuses with prenatal Zika virus infection showed retardation in brain maturation indexes evaluated by fetal MR. Brain calcifications were demonstrated by neurosonography in all cases, while fetal MR characterized the specific type of cortical development malformation.

The calculus of codes - From entropy, complexity, and information to life.

Exploring the core components that define living systems and their operational mechanisms within emerging biological entities is a complex endeavor. In the realm of biological systems literature, the terms matter, energy, information, complexity, and entropy are frequently referenced. However, possessing these concepts alone does not guarantee a comprehensive understanding or the ability to reconstruct the intricate nature of life. This study aims to illuminate the trajectory of these organic attributes, presenting a theoretical framework that delves into the integrated role of these concepts in biology. We assert that Code Biology serves as a pivotal steppingstone for unraveling the mechanisms underlying life. Biological codes (BCs) emerge not only from the interplay of matter and energy but also from Information. Contrary to deriving information from the former elements, we propose that information holds its place as a fundamental physical aspect. Consequently, we propose a continuum perspective called Calculus of Fundamentals involving three fundamentals: Matter, Energy, and Information, to depict the dynamics of BCs. To achieve this, we emphasize the necessity of studying Entropy and Complexity as integral organic descriptors. This perspective also facilitates the introduction of a mathematical theoretical framework that aids in comprehending continuous changes, the driving dynamics of biological fundamentals. We posit that Energy, Matter, and Information constitute the essential building blocks of living systems, and their interactions are governed by Entropy and Complexity analyses, redefined as biological descriptors. This interdisciplinary perspective of Code Biology sheds light on the intricate interplay between the controversial phenomenon of life and advances the idea of constructing a theory rooted in information as an organic fundamental.

Decoding semiotic minimal genome: a non-genocentric approach.

The search for the minimum information required for an organism to sustain a cellular system network has rendered both the identification of a fixed number of known genes and those genes whose function remains to be identified. The approaches used in such search generally focus their analysis on coding genomic regions, based on the genome to proteic-product perspective. Such approaches leave other fundamental processes aside, mainly those that include higher-level information management. To cope with this limitation, a non-genocentric approach based on genomic sequence analysis using language processing tools and gene ontology may prove an effective strategy for the identification of those fundamental genomic elements for life autonomy. Additionally, this approach will provide us with an integrative analysis of the information value present in all genomic elements, regardless of their coding status.

Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes.

In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found in 36 MDRAb isolates since 1986 till now. MLST technique allowed us to identify the presence of four different Clonal Complexes (109, 104, 119, 113) among the positive AbaR-type island positive strains. This is the first description of AbaR-type islands in the CC104 and CC113 that are the most widespread Clonal Complexes in Argentina. In addition, PCR mapping exposed different arrays to those previously described, evidencing the plasticity of this island. Our results evidence a widespread distribution of the AbaR-type genomic islands along the time in the MDRAb population, including the epidemic global clone 1 (GC1) as well as different clonal complexes to those already described in the literature.

Diverse mobilized class 1 integrons are common in the chromosomes of pathogenic Pseudomonas aeruginosa clinical isolates.

Eleven clinical class 1 integron-containing Pseudomonas aeruginosa isolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.

Class 2 integrons dissemination among multidrug resistance (MDR) clones of Acinetobacter baumannii.

Acinetobacter baumannii has emerged as a serious problem in the hospital environment at a global scale. Previous results from our laboratory showed a high frequency of class 2 integrons in A. baumannii strains from Argentina regarding the low rate of this element in A. baumannii isolates from the rest of the world. To reveal the current epidemiology of class 2 integrons, a molecular surveillance analyzing 78 multidrug resistant (MDR) A. baumannii isolates from Argentina and Uruguay was performed, exposing the presence of class 2 integron in the 36.61% of the isolates. Class 2 integron characterization showed that the typical Tn7::In2-7 array was present in 26 out of 27 intI2 positive isolates. All intI2 positive isolates contained at least one of the Tn7 transposition genes. In addition, we identified that 18 intI2 positive isolates possessed the Tn7::In2-7 within the attTn7 site. The molecular typing evidenced that clones I and IV that do not belong to widespread European clones I and II were found among the intI2 positive isolates. Our results exposed the widely dissemination of class 2 integron among MDR A. baumannii isolates from Argentina and Uruguay, also showing the persistence of two novel clones in our region, which could explain in part the high frequency of class 2 integron found in our region.

The versatility of Delftia sp. isolates as tools for bioremediation and biofertilization technologies.

Two Pb(II)-resistant bacteria isolated from a soil containing 2,500 mg/kg of Pb were identified by 16S rRNA sequencing analysis as Delftia sp. and designated as 3C and 6C. Both isolates grew at a Pb(II) concentration of 62 mg/L and at the stationary phase showed a Pb(II)-sorption capability of 10 ± 1.5 (3C) and 5 ± 0.8 (6C) mg/g of biomass. Biochemical properties related to heavy metal resistance and plant growth promotion were analyzed and compared with the Cr(VI)-resistant plant growth-promoting Delftia sp. JD2, previously reported by our group. Both isolates and JD2 were resistant to Cr(VI), Pb(II) and many antibiotics, produced siderophores and the phytohormone indole-3-acetic, and showed clover growth-promoting activity in greenhouse conditions. Interestingly, the occurrence of integron class 1 was shown in all isolates. Our results add to previous reports and suggest that bacteria of the genus Delftia could be consider as good candidates for the design of technologies for cleaning up contaminated environments and/or the production of biofertilizers.

Driver interactions lead changes in the distribution of imperiled terrestrial carnivores.

Biodiversity is dramatically declining worldwide due to the complex processes that include interactions among threats. Studies investigating how multiple drivers (inter)act to influence spatio-temporal shifts in species distribution ranges, which are among the most anticipated changes in biodiversity in the future, are still scarce in the scientific literature, particularly at meaningful conservation planning scales. We used species occurrence data for eight terrestrial Mediterranean carnivores at a regional scale of southern Spain to: 1) estimate environmental favourability to each species during two periods (1960s and present); 2) predict current favourability assuming the same environment-species relationships as the ones observed in the 1960s (expected favourability); and 3) analyse single and interactive effects of human persecution, presence of protected areas, and prey richness on favourability changes (present vs. expected) for each carnivore species. We found that, with a few exceptions, environmentally favourable areas for carnivore occurrence were more widely distributed in the past than today and, for most species, favourability tended to increase inside protected areas, with low frequency of poisoning events and high prey richness. Notwithstanding, for rare species such as Iberian grey wolf (Canis lupus signatus) and Iberian lynx (Lynx pardinus), interactions among drivers were the most important predictors of favourability changes, underpinned by a compensatory role of protected areas in the face of continued human persecution. We emphasize the role of protected areas in abating the effects of biodiversity threats and claim that scientific studies based on analyses of single-effect drivers that omit driver interactions may misinform conservation planning and require revision.

Genotoxicity and Reproductive Risk in Workers Exposed to Pesticides in Rural Areas of Curicó, Chile: A Pilot Study.

Significant risks to human health have been associated with chronic exposure to low doses of pesticides, a situation which may be frequent among agricultural workers. In this context, and regarding the agricultural-based economy of central Chile, we aimed to explore the genotoxic damage in agricultural workers and reproductive risk among women in rural and urban areas of Curicó, a traditional agricultural district in Chile. Hence, we sampled a group of rural agricultural workers associated with pesticide management (n = 30) and an urban unexposed group (n = 30). Our results showed that the agricultural workers had higher micronuclei frequencies (MN: ß = 13.27; 95% CI low = 11.08, CI high = 15.47) and women had a 40-fold higher risk of reproductive problems (OR = 40.32; 95% CI low = 2.60, CI high = 624.31) than the unexposed group. The factor analysis of mixed data (FAMD) showed that neither the sex nor smoking habits appear to define the ordination of the data. Nevertheless, the exposure level did segregate them in the multidimensional space (explained variance: 35.38% dim-1; 18.63% dim-2). This pilot study highlights the higher risks of biological conditions negatively associated with the health of agricultural workers.

Diploid genome assembly of Kluyveromyces marxianus NRRL Y-50883 (SLP1).

The yeast Kluyveromyces marxianus SLP1 has the potential for application in biotechnological processes because it can metabolize several sugars and produce high-value metabolites. K. marxianus SLP1 is a thermotolerant yeast isolated from the mezcal process, and it is tolerant to several cell growth inhibitors such as saponins, furan aldehydes, weak acids, and phenolics compounds. The genomic differences between dairy and nondairy strains related to K. marxianus variability are a focus of research attention, particularly the pathways leading this species toward polyploidy. We report the diploid genome assembly of K. marxianus SLP1 nonlactide strain into 32 contigs to reach a size of ∼12 Mb (N50 = 1.3 Mb) and a ∼39% GC content. Genome size is consistent with the k-mer frequency results. Genome annotation by Funannotate estimated 5000 genes in haplotype A and 4910 in haplotype B. The enriched annotated genes by ontology show differences between alleles in biological processes and cellular component. The analysis of variants related to DMKU3 and between haplotypes shows changes in LAC12 and INU1, which we hypothesize can impact carbon source performance. This report presents the first polyploid K. marxianus strain recovered from nonlactic fermenting medium.

Dissemination of multiple drug resistance genes by class 1 integrons in Klebsiella pneumoniae isolates from four countries: a comparative study.

A comparative genetic analysis of 42 clinical Klebsiella pneumoniae isolates, resistant to two or more antibiotics belonging to the broad-spectrum ß-lactam group, sourced from Sydney, Australia, and three South American countries is presented. The study focuses on the genetic contexts of class 1 integrons, mobilizable genetic elements best known for their role in the rapid evolution of antibiotic resistance among Gram-negative pathogens. It was found that the class 1 integrons in this cohort were located in a number of different genetic contexts with clear regional differences. In Sydney, IS26-associated Tn21-like transposons on IncL/M plasmids contribute greatly to the dispersal of integron-associated multiple-drug-resistant (MDR) loci. In contrast, in the South American countries, Tn1696-like transposons on an IncA/C plasmid(s) appeared to be disseminating a characteristic MDR region. A range of mobile genetic elements is clearly being recruited by clinically important mobile class 1 integrons, and these elements appear to be becoming more common with time. This in turn is driving the evolution of complex and laterally mobile MDR units and may further complicate antibiotic therapy.

[VIM-2 metallo-ß-lactamase gen detection in a class 1 integron associated to bla(CTX-M-2) in a Pseudomonas aeruginosa clinical isolate in Uruguay: first communication]. / Detección del gen codificante de la metalo-ß-lactamasa VIM-2 en un integrón de clase 1 asociado con el gen blaCTX-M-2 en un aislamiento clínico de Pseudomonas aeruginosa en el Uruguay: primera comunicación.

In order to analyze the presence of metallo-ß-lactamase in our country, we included in this study Pseudomonas aeruginosa isolates causing nosocomial infections in a hospital from Uruguay. The presence of a metallo-ß-lactamase VIM-2 in a class 1 integron and of an extended spectrum -lactamase CTX-M-2 was detected in one isolate. This is the first report of both genes, bla(CTX-M-2) and bla(VIM-2),in the same P. aeruginosa isolate. Although carbapenemases have been extensively documented in the world, this is the first report of an acquired metallo-ß-lactamase with carbapenemase activity in pathogenic bacteria in Uruguay.

In Vivo High Plasticity of Multi-Drug Resistant ST258 Klebsiella pneumoniae.

Carbapenemase production in Enterobacterales clinical isolates is a global threat. Multi-drug resistant Klebsiella pneumoniae harboring carbapenemases are a major concern among the hospital settings in Latin America. Aim: The aim of this study was to analyze the genetic relatedness between three isolates of K. pneumoniae recovered from one patient in the same bacteriological round on the same day, which exhibited different susceptibility profiles to carbapenems (CP) and to colistin (Col). Isolates' profiles were as follows (susceptible-S/resistant-R): CPS/ColR, CPR/ColR, and CPR/ColS. Pulse-field gel electrophoresis, multilocus sequence typing, and whole genome sequencing were performed. Conjugation assays were carried out and PCR determination in transconjugants (Tcs) was made for: blaCTX-M-groups, blaNDM, blaKPC, blaTEM, qnr alleles, aac(6')Ib-cr, ermB, and plasmid incompatibility groups (Inc). Results: All isolates belonged to the same clone, to ST258 and harbored blaCTX-M-14, blaCTX-M-15, qnrA1, qnrB1, aac(6')Ib-cr, and wzi154 (capsule-locus KL107). One isolate had additional wzi gene, wzi109 (capsule-locus KL36). In CPR isolates, the pattern was explained for blaNDM-1 or blaNDM-1/blaKPC-2 presence, and in ColR for IS5-like element insertion in mgrB at different positions. Co-mobilization of blaNDM-1/qnrA1 was associated to a different plasmid Inc (A/C-FII) in both blaNDM-1 donors. Mobilization of blaCTX-M-14 was related to IncI1 in one donor. Conclusion: These findings highlight the potential plasticity of ST258 K. pneumoniae clone. To the best of our knowledge, this is the first description of blaNDM-1/blaKPC-2-producing K. pneumoniae ST258 in Latin America.

Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection.

A class 2 integron was found in an Escherichia coli isolate mediating a urinary tract infection. Unlike other class 2 integrons from pathogens, the encoded IntI2 protein was functional. The integron possessed a dfrA14 cassette, and a second novel cassette in which a lipoprotein signal peptidase gene is predicted.

Urinary tract infections in a South American population: dynamic spread of class 1 integrons and multidrug resistance by homologous and site-specific recombination.

One hundred four bacterial strains mediating urinary tract infections in separate individuals from a Uruguayan community were isolated. Forty-six strains conferred a multidrug resistance phenotype. All 104 strains were examined for the presence of class 1, 2, and 3 integrons. Class 1 integrons were found in 21 isolates across four distinct bacterial genera. A large class 1 integron in a Klebsiella pneumoniae strain was fully sequenced and was 29,093 bp in length. This integron probably arose by homologous recombination since it was embedded in a hybrid Tn21-like transposon backbone which comprised a Tn5036-like tnp transposition module at the IRi integron end and a Tn21 mer module at the IRt integron end. The parent integron/transposon that contributed the Tn5036 module was not related to Tn1696 since the integron insertion points in the transposon backbones were 16 bases apart. Examination of the other 20 class 1 integron-containing strains revealed further evidence of genetic exchange. This included a strain that possessed a Tn5036 module at the IRt end but not at the IRi end and another that possessed a tnp module beyond IRi that was a hybrid of Tn21 and Tn5051 and that is presumed to have arisen by site-specific recombination. This study highlights the ability of different genetic elements to act cooperatively to spread and rearrange antibiotic resistance in a community.