Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction.

Natural proteins are frequently marginally stable, and an increase in environmental temperature can easily lead to unfolding. As a result, protein engineering to improve protein stability is an area of intensive research. Nonetheless, since there is usually a high degree of structural homology between proteins from thermophilic organisms and their mesophilic counterparts, the identification of structural determinants for thermoadaptation is challenging. Moreover, in many cases, it has become clear that the success of stabilization strategies is often dependent on the evolutionary history of a protein family. In the last few years, the use of ancestral sequence reconstruction (ASR) as a tool for elucidation of the evolutionary history of functional traits of a protein family has gained strength. Here, we used ASR to trace the evolutionary pathways between mesophilic and thermophilic kinases that participate in the biosynthetic pathway of vitamin B1 in bacteria. By combining biophysics approaches, X-ray crystallography, and molecular dynamics simulations, we found that the thermal stability of these enzymes correlates with their kinetic stability, where the highest thermal/kinetic stability is given by an increase in small hydrophobic amino acids that allow a higher number of interatomic hydrophobic contacts, making this type of interaction the main support for stability in this protein architecture. The results highlight the potential benefits of using ASR to explore the evolutionary history of protein sequence and structure to identify traits responsible for the kinetic and thermal stability of any protein architecture.

Intelligent Learning-Based Methods for Determining the Ideal Team Size in Agile Practices.

One of the significant challenges in scaling agile software development is organizing software development teams to ensure effective communication among members while equipping them with the capabilities to deliver business value independently. A formal approach to address this challenge involves modeling it as an optimization problem: given a professional staff, how can they be organized to optimize the number of communication channels, considering both intra-team and inter-team channels? In this article, we propose applying a set of bio-inspired algorithms to solve this problem. We introduce an enhancement that incorporates ensemble learning into the resolution process to achieve nearly optimal results. Ensemble learning integrates multiple machine-learning strategies with diverse characteristics to boost optimizer performance. Furthermore, the studied metaheuristics offer an excellent opportunity to explore their linear convergence, contingent on the exploration and exploitation phases. The results produce more precise definitions for team sizes, aligning with industry standards. Our approach demonstrates superior performance compared to the traditional versions of these algorithms.

Structural insights into a functional unit from an immunogenic mollusk hemocyanin.

Mollusk hemocyanins, among the largest known proteins, are used as immunostimulants in biomedical and clinical applications. The hemocyanin of the Chilean gastropod Concholepas concholepas (CCH) exhibits unique properties, which makes it safe and effective for human immunotherapy, as observed in animal models of bladder cancer and melanoma, and dendritical cell vaccine trials. Despite its potential, the structure and amino acid sequence of CCH remain unknown. This study reports two sequence fragments of CCH, representing three complete functional units (FUs). We also determined the high-resolution (1.5 Å) X-ray crystal structure of an "FU-g type" from the CCHB subunit. This structure enables in-depth analysis of chemical interactions at the copper-binding center and unveils an unusual, truncated N-glycosylation pattern. These features are linked to eliciting more robust immunological responses in animals, offering insights into CCH's enhanced immunostimulatory properties and opening new avenues for its potential applications in biomedical research and therapies.

The Severity of Initial Unilateral Cleft Lip and Nasal Deformity Predicts Long-Term Postoperative Esthetic Outcome.

BACKGROUND: Infantile cleft lip and nasal severity influence the final esthetic result of the repair. Although various authors have described methods of cleft lip and nasal repair, there is a paucity of data that correlates cleft severity with esthetic outcomes. The aim of this study was to examine the correlation between presurgical severity of unilateral cleft deformity and long-term postoperative esthetic outcomes. METHODS: This retrospective study, based at a single institution, investigated patients with complete unilateral cleft lip, with or without cleft palate, who underwent repair by a single surgeon, had preoperative infantile facial casts, and had postoperative facial photographs at 6 to 11 years of age (N=31). Preoperative nostril width ratio and columellar angle measurements were taken from facial casts. Postoperative, long-term nasolabial appearance was rated by 5 blinded observers used a modified Kuijpers-Jagtman scale. Linear regression was used to determine the relationship between preoperative cleft severity and postoperative ratings. RESULTS: Preoperative nostril width ratio directly correlated with postoperative nasal form score (r=0.40; P=0.026); likewise, preoperative columellar angle predicted postoperative nasal form score (r=0.37; P=0.040). Preoperative cleft severity was not significantly correlated with vermillion border appearance. Cronbach α values of 0.91 (nasal form) and 0.79 (vermillion border) indicated good inter-rater reliability. Kappa values of 0.87 (nasal form) and 0.70 (vermillion border) indicated good intrarater reliability. CONCLUSIONS: Preoperative unilateral cleft nose severity directly correlates with long-term postoperative nasal appearance in childhood. Outcome studies should present and control for preoperative severity to allow more accurate assessment of repair techniques.

Relationship between inspiratory muscle strength and balance in women: A cross-sectional study.

BACKGROUND: There is scarce evidence on changes at the functional level associated with the respiratory area in women. This study aims to analyse the relationship between inspiratory muscle strength and balance in women. MATERIAL AND METHODS: In this cross-sectional observational study, the sample consisted of groups according to the results obtained in the balance test. Inspiratory muscle weakness was defined as maximum inspiratory pressure (MIP) ≤ 80% of the predictive value. MIP was carried out using through a mouthpiece, with an electronic manometer. Logistic regression model was used to examine if MIP predicts balance. RESULTS: 159 women participated in the study. Approximately 20% of them achieved balance ≤ 2 seconds and 18% presented MIP≤80%. MIP was associated with the time achieved in the one-leg support test. Subjects with MIP ≤ 80% of the predictive value show 3 times more risk of having a lower performance in the balance test (OR = 3.26). CONCLUSIONS: Inspiratory muscle weakness is associated with deficient balance in this sample. It shows the need for multidimensional assessment and rehabilitation strategies for patients identified as having MIP weakness and/or balance disorders.

Employees Perceptions of Job Insecurity and Performance: A Qualitative Approach.

The purpose of this article is to understand the experience of workers' perceptions of job insecurity and its relation to performance. To this end, we conducted semi-structured interviews with 38 workers in the retail, services, education, financial, construction, and pharmaceutical industries in Chile. Using content analysis based on workers' accounts of their own experience, we identified two main categories: (a) the experience of job insecurity viewed in relation to the context of the COVID-19 pandemic and emotional aspects of job insecurity, and (b) the relation between job insecurity and performance. The possibility of job loss expresses itself in experiences and emotions that are related to the performance of workers in different ways. These findings are discussed in terms of stress theory and the motivation to preserve jobs.

Imparting Fire Retardancy and Smoke Suppression to Leather during Tanning Processes.

Leather is considered a luxury good when used in seating and upholstery. To improve safety, flame retardancy in leather is usually achieved through various finishing processes such as spray or roller coating. These treatments require processing steps that cost time and are labor-intensive. One avenue to achieving flame retardancy in leather is to add flame retardants during the tanning process. However, the influence on flame retardancy exerted by specific intumescent additives specifically added during leather tanning has yet to be investigated. This work explores the roles played by intumescent additive compounds in flame retarding leather when they are added during tanning instead of applied as a coating. Via a systematic investigation of various compound mixtures, the flame retardant effects in the condensed and the gas phases are elucidated. The results show a strong impact of melamine in the gas phase and of polyphosphates in the condensed phase. Their impact was quantified in fire and smoke analysis, showing a 14% reduction in the peak of heat release rate, strongly reduced burning lengths, and a 20% reduction in total smoke release compared to nontreated leather. These results illuminate the key role played by specific compounds in the flame retardancy of leather, particularly when they are added specifically during the tanning process instead of being applied as a coating. This method has great potential to reduce processing steps, lower costs, and improve material safety.

[Evaluation of sexual issues by professionals who assist type 2 diabetic men]. / Evaluación de temas sexuales por profesionales que asisten a hombres con diabetes tipo 2.

INTRODUCTION: Our objective was to assess whether physicians who care for people with type 2 diabetes address andrological symptoms such as erectile sexual dysfunction, decreased libido, and symptoms and/or signs of hypogonadism. METHODS: An anonymous survey was carried out with 171 doctors, 113 were females (66.1%), the mean age was 46 ± 10 years (females: 45 ± 10 and males: 49 ± 10, p = 0.006). RESULTS: There were no differences in responses according to gender. Regarding the presence of erectile sexual dysfunction and/or decreased libido, 44.4% (n = 76) and 55.6% (n = 95) did not ask about them, respectively. In patients with symptoms of hypogonadism, 50.9% (n = 87) did not request a testosterone measurement. Regarding the improvement of the metabolic profile of type 2 diabetes mellitus and sexual symptoms after replacement with testosterone, 65.8% of the respondents answered that both conditions could improve after treatment. In the presence of symptoms compatible with hypogonadism, 74.7% of those surveyed stated that the measurement of testosterone should be performed. A total of 108 (63.2%) showed interest in being trained on topics related to type 2 diabetes and disorders of the sexual sphere. CONCLUSION: A large percentage of physicians who take care of men with type 2 diabetes do not inquire about andrological disorders. It is necessary to raise awareness and train doctors to detect, treat and/or refer these frequent health problems, not only to improve the quality of life of patients but also to effectively respond and prevent a major health problem.

Introducción: Los trastornos andrológicos son frecuentes en varones con diabetes tipo 2. El objetivo fue evaluar si los médicos que atienden a personas con diabetes tipo 2 abordan problemas andrológicos como disfunción sexual eréctil, disminución de libido y síntomas de hipogonadismo. Métodos: Se llevó a cabo una encuesta anónima a 171 médicos, de ellos 113 fueron mujeres (66.1%) con una edad media de 46 ± 10 años (mujeres: 45 ± 10 y varones: 49 ± 10, p = 0.006). Resultados: No hubo diferencias en las respuestas según el género. El 44.4% (n = 76) y el 55.6% (n = 95) no preguntan sobre la presencia de disfunción sexual eréctil y/o disminución de libido, respectivamente. El 50.9% (n = 87) no solicitó medición de testosterona en pacientes con síntomas de hipogonadismo. El 65.8% de los participantes respondió que el reemplazo con testosterona puede mejorar el perfil metabólico de la diabetes mellitus tipo 2 y los síntomas sexuales. El 74.7% de los encuestados afirmó que la medición de testosterona debería realizarse ante la presencia de síntomas compatibles con hipogonadismo. El 63.2% (n = 108) mostró interés en formación sobre temas relacionados a diabetes tipo 2 y trastornos de la esfera sexual. Conclusión: Un gran porcentaje de médicos que asisten a varones con diabetes tipo 2 no indaga sobre trastornos andrológicos. Es necesario concientizar y entrenar a los médicos, para detectar, tratar y/o derivar estos problemas de salud tan frecuentes, no solo para mejorar la calidad de vida de los pacientes sino para responder y prevenir efectivamente a un problema mayor de salud.

Evaluación de temas sexuales por profesionales que asisten a hombres con diabetes tipo 2 / Evaluation of sexual issues by professionals who assist type 2 diabetic men

Resumen Introducción: Los trastornos andrológicos son frecuentes en varones con diabetes tipo 2. El objetivo fue evaluar si los médicos que atienden a personas con diabetes tipo 2 abordan problemas andro lógicos como disfunción sexual eréctil, disminución de libido y síntomas de hipogonadismo. Métodos: Se llevó a cabo una encuesta anónima a 171 médicos, de ellos 113 fueron mujeres (66.1%) con una edad media de 46 ± 10 años (mujeres: 45 ± 10 y varones: 49 ± 10, p = 0.006). Resultados: No hubo diferencias en las res puestas según el género. El 44.4% (n = 76) y el 55.6% (n = 95) no preguntan sobre la presencia de disfunción sexual eréctil y/o disminución de libido, respectivamente. El 50.9% (n = 87) no solicitó medición de testosterona en pacientes con síntomas de hipogonadismo. El 65.8% de los participantes respondió que el reemplazo con testosterona puede mejorar el perfil metabólico de la diabetes mellitus tipo 2 y los síntomas sexuales. El 74.7% de los encuestados afirmó que la medición de testosterona debería realizarse ante la presencia de síntomas compatibles con hipogonadismo. El 63.2% (n = 108) mostró interés en formación sobre temas relacionados a diabetes tipo 2 y trastornos de la esfera sexual. Conclusión: Un gran porcentaje de médicos que asisten a varones con diabetes tipo 2 no indaga sobre trastornos andrológicos. Es necesario concientizar y entrenar a los médicos, para detectar, tratar y/o derivar estos problemas de salud tan frecuentes, no solo para mejorar la calidad de vida de los pacientes sino para responder y prevenir efectivamente a un problema mayor de salud.

Abstract Introduction: Our objective was to assess whether physicians who care for people with type 2 dia betes address andrological symptoms such as erectile sexual dysfunction, decreased libido, and symptoms and/ or signs of hypogonadism. Methods: An anonymous survey was carried out with 171 doctors, 113 were females (66.1%), the mean age was 46 ± 10 years (females: 45 ± 10 and males: 49 ± 10, p = 0.006). Results: There were no differences in responses according to gender. Regarding the presence of erectile sexual dysfunction and/or decreased libido, 44.4% (n = 76) and 55.6% (n = 95) did not ask about them, respectively. In patients with symptoms of hypogonadism, 50.9% (n = 87) did not request a testosterone measurement. Regarding the improvement of the metabolic profile of type 2 diabetes mellitus and sexual symptoms after replacement with testosterone, 65.8% of the respondents answered that both conditions could improve after treatment. In the presence of symptoms compatible with hypogonadism, 74.7% of those surveyed stated that the measurement of testosterone should be performed. A total of 108 (63.2%) showed interest in being trained on topics related to type 2 diabetes and disorders of the sexual sphere. Conclusion: A large percentage of physicians who take care of men with type 2 diabetes do not inquire about andrological disorders. It is necessary to raise awareness and train doctors to detect, treat and/or refer these frequent health problems, not only to improve the quality of life of patients but also to effectively respond and prevent a major health problem.

Ca2+ signalling system initiated by endoplasmic reticulum stress stimulates PERK activation.

The accumulation of unfolded proteins within the Endoplasmic Reticulum (ER) activates a signal transduction pathway termed the unfolded protein response (UPR), which attempts to restore ER homoeostasis. If this cannot be done, UPR signalling ultimately induces apoptosis. Ca2+ depletion in the ER is a potent inducer of ER stress. Despite the ubiquity of Ca2+ as an intracellular messenger, the precise mechanism(s) by which Ca2+ release affects the UPR remains unknown. Tethering a genetically encoded Ca2+ indicator (GCamP6) to the ER membrane revealed novel Ca2+ signalling events initiated by Ca2+ microdomains in human astrocytes under ER stress, induced by tunicamycin (Tm), an N-glycosylation inhibitor, as well as in a cell model deficient in all three inositol triphosphate receptor isoforms. Pharmacological and molecular studies indicate that these local events are mediated by translocons and that the Ca2+ microdomains impact (PKR)-like-ER kinase (PERK), an UPR sensor, activation. These findings reveal the existence of a Ca2+ signal mechanism by which stressor-mediated Ca2+ release regulates ER stress.

Untangling Galectin-Mediated Circuits that Control Hypoxia-Driven Angiogenesis.

Development of an aberrant vascular network is a hallmark of the multistep pathological process of tumor growth and metastasis. In response to hypoxia, several pro-angiogenic factors are synthesized to support vascularization programs required for cancer progression. Emerging data indicate the involvement of glycans and glycan-binding proteins as critical regulators of vascular circuits in health and disease. Galectins may be regulated by hypoxic conditions and control angiogenesis in different physiopathological settings. These ß-galactoside-binding proteins may promote sprouting angiogenesis by interacting with different glycosylated receptors and triggering distinct signaling pathways. Understanding the role of galectins in tumor neovascularization will contribute to the design of novel anti-angiogenic therapies aimed at complementing current anti-cancer modalities and overcoming resistance to these treatments. Here we describe selected strategies and methods used to study the role of hypoxia-regulated galectins in the regulation of blood vessel formation.

Structural and evolutionary analysis unveil functional adaptations in the promiscuous behavior of serum albumins.

Promiscuous activities have been related to the capacity to catalyze reactions different from those a protein has evolved to sustain. In this work, we rethought the serum albumin's promiscuous behavior using evolutionary and structural analysis. We found that the cross aldol condensation of acetone and p-formylbenzonitrile is a promiscuous reaction conserved in humans serum albumin and in closely related albumins from other mammals. Evolutionary analysis indicates that the residues involved in this promiscuous reaction are evolving under positive selection, an evolutionary pattern indicating a putative functional adaptation. Also, key residues are located in an evolutionary conserved cavity connected with the protein surface with an also conserved tunnel and mutations involving these residues are described in human diseases. Overall, our results suggest that albumin could have evolved to sustain a still unknown biological function among the many others it maintains. Our results could contribute to better characterize the serum albumin family and raise questions about the evolution of protein promiscuity and function.

Clinical characteristics and in-hospital mortality of patients with COVID-19 in Chile: A prospective cohort study.

AIMS OF THIS STUDY: To describe the Latin American population affected by COVID-19, and to determine relevant risk factors for in-hospital mortality. METHODS: We prospectively registered relevant clinical, laboratory, and radiological data of adult patients with COVID-19, admitted within the first 100 days of the pandemic from a single teaching hospital in Santiago, Chile. The primary outcome was in-hospital mortality. Secondary outcomes included the need for respiratory support and pharmacological treatment, among others. We combined the chronic disease burden and the severity of illness at admission with predefined clinically relevant risk factors. Cox regression models were used to identify risk factors for in-hospital mortality. RESULTS: We enrolled 395 adult patients, their median age was 61 years; 62.8% of patients were male and 40.1% had a Modified Charlson Comorbidity Index (MCCI) ≥5. Their median Sequential Organ Failure Assessment (SOFA) score was 3; 34.9% used a high-flow nasal cannula and 17.5% required invasive mechanical ventilation. The in-hospital mortality rate was 14.7%. In the multivariate analysis, were significant risk factors for in-hospital mortality: MCCI ≥5 (HR 4.39, P < .001), PaO2 /FiO2 ratio ≤200 (HR 1.92, P = .037), and advanced chronic respiratory disease (HR 3.24, P = .001); pre-specified combinations of these risk factors in four categories was associated with the outcome in a graded manner. CONCLUSIONS AND CLINICAL IMPLICATIONS: The relationship between multiple prognostic factors has been scarcely reported in Latin American patients with COVID-19. By combining different clinically relevant risk factors, we can identify COVID-19 patients with high-, medium- and low-risk of in-hospital mortality.

Acute liver failure due to herpes simplex virus: diagnostic clues and potential role of plasmapheresis: A case report.

INTRODUCTION: Acute liver failure (ALF) is a life-threatening condition that remains challenging for physicians despite several advances in supportive care. Etiologies vary worldwide, with herpes simplex virus (HSV) hepatitis representing less than 1% of cases. Despite its low incidence, ALF is a lethal cause of acute necrotizing hepatitis and has a high mortality. Early antiviral treatment is beneficial for survival and decreased liver transplantation necessity. However, plasmapheresis, despite its theoretical potential benefit, is scarcely reported. PATIENT CONCERNS: A 25-year-old woman with no known disease presented with painful pharynx ulcers, increased transaminases and impaired liver function. DIAGNOSIS: ALF due to a disseminated HSV-2 primary infection was diagnosed with a positive polymerase chain reaction for HSV-2 in the biopsied liver tissue and blood. INTERVENTIONS: Empiric antiviral treatment was initiated. After clinical deterioration, plasmapheresis was also initiated. OUTCOMES: After 6 cycles of plasmapheresis and supportive care, the patient's condition improved without undergoing liver transplantation. CONCLUSIONS: ALF is a life-threatening condition, and HSV as an etiology must be suspected based on background, clinical manifestation, and laboratory information. The potential role of plasmapheresis in HSV hepatitis should be considered.

Acute mild dim light at night slightly modifies sleep but does not affect glucose homeostasis in healthy men.

OBJECTIVE: We evaluated the effect of acute mild light exposure at night on sleep architecture and glucose homeostasis. PATIENTS/METHODS: Twenty healthy normal-weight men took part in two conditions of a randomized, controlled, balanced cross-over experimental study: i) two-consecutive nights with 8-h of sleep under dLAN (<5 lux) or ii) total darkness (CON). Sleep was evaluated by polysomnography. In the morning following 'night2', glucose homeostasis was assessed by an intravenous glucose tolerance test (ivGTT) with consecutive measures of glucose, insulin, and c-peptide. Plasma cortisol was measured at night before sleep, after morning awakening, and during mid-afternoon hours. RESULTS: There was no significant difference in total sleep time, sleep efficiency, and sleep latency between conditions (all p > 0.66). However, NREM sleep stage N3 latency was prolonged after dLAN (p = 0.02) and NREM sleep stage 2 was decreased after two nights with dLAN (p = 0.04). During the first sleep hour, power in slow-oscillations, slow-waves, and delta bands diminished after dLAN (all p < 0.04). Glucose, insulin, and c-peptide were not altered by dLAN (all p > 0.14). Cortisol was reduced in the afternoon after 'night1' and in the morning after 'night2' (both p < 0.03). CONCLUSIONS: dLAN slightly disturbed sleep architecture and quality without impairment of glucose homeostasis. Longer exposure to chronic dLAN might be needed to unmask its hypothesized metabolic consequences.

Adaptación transcultural y validación al español de la escala de movilidad funcional DEMMI (DeMorton Mobility Index) para adultos mayores / Transcultural adaptation and validation to spanish of the DEMMI functional mobility scale (DeMorton Mobility Index) for older adults

Introducción: el Índice de Movilidad de De Morton® (en inglés De Morton Mobility Index: DEMMI®) es una escala, válida y fiable para evaluar la movilidad funcional del adulto mayor. Objetivo: validar una versión en español para pacientes hospitalizados en una sala general. Material y métodos: traducción y adaptación transcultural, evaluación de la fiabilidad interobservador y validación de criterio explorando la correlación entre los índices DEMMI y Barthel® al ingreso hospitalario y también entre la percepción subjetiva del cambio en la movilidad por parte del propio paciente y la del puntaje DEMMI, y además evaluando la asociación entre este y el grado de acompañamiento requerido en el egreso hospitalario (n = 87). Su consistencia interna fue evaluada mediante los coeficientes de Kuder y Richardson (KR) y de Cronbach (n = 104). Resultados: la correlación entre los puntajes DEMMI y Barthel fue buena (Spearman's Rho = 0,78: p ≤ 0,0001), mientras que la correlación entre la percepción del paciente respecto del cambio en su movilidad y la variación en el puntaje DEMMI fue moderada (Spearman's Rho = 0,50; p < 0,0001). Quienes fueron dados de alta con alto nivel de acompañamiento habían tenido al ingreso un puntaje DEMMI inferior (28,1; IC 95%, 24,9 a 31,3) al de quienes no lo requirieron (48; 44,4 a 53,0). La consistencia interna fue adecuada (KR = 0,827 y Cronbach = 0,745; Pearson's Rho = 0,7885; p < 0,00001). Conclusión: la consistencia interna y la fiabilidad interobservador de la versión en español del puntaje DEMMI son buenas, mientras que sus cambios tienen buena correlación con los percibidos por los propios pacientes. Consideramos que puede ser usado como un elemento más para estimar al momento del ingreso hospitalario, el grado de acompañamiento que requerirán al ser dados de alta. (AU)

Introduction: the De Morton Mobility Index (DEMMI) is a valid and reliable scale to evaluate the functional mobility of the elderly. Aim: validate a Spanish version for hospitalized patients in a general ward. Material and methods: translation and cross-cultural adaptation, evaluation of inter-observer reliability and criterion validation exploring the correlation between DEMMI and Barthel scores at hospital admission and also between the subjective perception of the change in mobility by the patient himself and that of DEMMI score, and also, evaluating the association between DEMMI and the degree of support required at hospital discharge (n = 87). Its internal consistency was evaluated using Kuder-Richardson (KR) and Cronbach (n = 104) coefficients. Results: correlation between DEMMI and Barthel scores was good (Spearman's Rho = 0.78: p < = 0.0001), while correlation between patient's perception of change in mobility and variation in DEMMI score was moderate (Spearman's Rho = 0.50; p < 0.0001). Those discharged with a high level of support had a lower DEMMI score upon admission (28.1; 95% CI 24.9 to 31.3) than those who didn´t require it (48; 44.4 to 53.0). Internal consistency was adequate (KR = 0.827 and Cronbach = 0.745; Pearson's Rho = 0.7885; p < 0.00001). Conclusion: internal consistency and interobserver reliability of the Spanish version of DEMMI score are good, while its changes correlate well with those perceived by the patients themselves. We consider that it can be used as another element to estimate at hospital admission, the degree of support they will require upon discharge. (AU)

Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes.

ADP-dependent kinases were first described in archaea, although their presence has also been reported in bacteria and eukaryotes (human and mouse). This enzyme family comprises three substrate specificities; specific phosphofructokinases (ADP-PFKs), specific glucokinases (ADP-GKs), and bifunctional enzymes (ADP-PFK/GK). Although many structures are available for members of this family, none exhibits fructose-6-phosphate (F6P) at the active site. Using an ancestral enzyme, we obtain the first structure of an ADP-dependent kinase (AncMsPFK) with F6P at its active site. Key residues for sugar binding and catalysis were identified by alanine scanning, D36 being a critical residue for F6P binding and catalysis. However, this residue hinders glucose binding because its mutation to alanine converts the AncMsPFK enzyme into a specific ADP-GK. Residue K179 is critical for F6P binding, while residues N181 and R212 are also important for this sugar binding, but to a lesser extent. This structure also provides evidence for the requirement of both substrates (sugar and nucleotide) to accomplish the conformational change leading to a closed conformation. This suggests that AncMsPFK mainly populates two states (open and closed) during the catalytic cycle, as reported for specific ADP-PFK. This situation differs from that described for specific ADP-GK enzymes, where each substrate independently causes a sequential domain closure, resulting in three conformational states (open, semiclosed, and closed).

Birds breathe at an aerodynamic resonance.

We present a dynamical model for the avian respiratory system and report the measurement of its variables in normal breathing canaries (Serinus canaria). Fitting the parameters of the model, we are able to show that the birds in our study breathe at an aerodynamic resonance of their respiratory system. For different respiratory regimes, such as singing, where rapid respiratory gestures are used, the nonlinearities of the model lead to a shift in its resonances toward higher frequency values.

An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages.

Population-level sampling and whole-genome sequences of different individuals allow one to identify signatures of hybridization, gene flow and potential molecular mechanisms of environmental responses. Here, we report the isolation of 160 Saccharomyces eubayanus strains, the cryotolerant ancestor of lager yeast, from ten sampling sites in Patagonia along 2,000 km of Nothofagus forests. Frequency of S. eubayanus isolates was higher towards southern and colder regions, demonstrating the cryotolerant nature of the species. We sequenced the genome of 82 strains and, together with 23 available genomes, performed a comprehensive phylogenetic analysis. Our results revealed the presence of five different lineages together with dozens of admixed strains. Various analytical methods reveal evidence of gene flow and historical admixture between lineages from Patagonia and Holarctic regions, suggesting the co-occurrence of these ancestral populations. Analysis of the genetic contribution to the admixed genomes revealed a Patagonian genetic origin of the admixed strains, even for those located in the North Hemisphere. Overall, the Patagonian lineages, particularly the southern populations, showed a greater global genetic diversity compared to Holarctic and Chinese lineages, in agreement with a higher abundance in Patagonia. Thus, our results are consistent with a likely colonization of the species from peripheral glacial refugia from South Patagonia. Furthermore, fermentative capacity and maltose consumption resulted negatively correlated with latitude, indicating better fermentative performance in northern populations. Our genome analysis, together with previous reports in the sister species S. uvarum suggests that a S. eubayanus ancestor was adapted to the harsh environmental conditions of Patagonia, a region that provides the ecological conditions for the diversification of these ancestral lineages.

Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates.

The utilization of S. eubayanus has recently become a topic of interest due to the novel organoleptic properties imparted to beer. However, the utilization of S. eubayanus in brewing requires the comprehension of the mechanisms that underlie fermentative differences generated from its natural genetic variability. Here, we evaluated fermentation performance and volatile compound production in ten genetically distinct S. eubayanus strains in a brewing fermentative context. The evaluated strains showed a broad phenotypic spectrum, some of them exhibiting a high fermentation capacity and high levels of volatile esters and/or higher alcohols. Subsequently, we obtained molecular profiles by generating 'end-to-end' genome assemblies, as well as metabolome and transcriptome profiling of two Patagonian isolates exhibiting significant differences in beer aroma profiles. These strains showed clear differences in concentrations of intracellular metabolites, including amino acids, such as valine, leucine and isoleucine, likely impacting the production of 2-methylpropanol and 3-methylbutanol. These differences in the production of volatile compounds are attributed to gene expression variation, where the most profound differentiation is attributed to genes involved in assimilatory sulfate reduction, which in turn validates phenotypic differences in H2 S production. This study lays a solid foundation for future research to improve fermentation performance and select strains for new lager styles based on aroma and metabolic profiles.