MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.

Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despite many successful applications, MDFF is still limited by its high computational cost, overfitting, accuracy, and performance issues due to entrapment within wrong local minima. Modern ensemble-based MDFF tools have generated promising results in the past decade. In line with these studies, we present MDFF_NM, a stochastic hybrid flexible fitting algorithm combining Normal Mode Analysis (NMA) and simulation-based flexible fitting. Initial tests reveal that, besides accelerating the fitting process, MDFF_NM increases the diversity of fitting routes leading to the target, uncovering ensembles of conformations in closer agreement with experimental data. The potential integration of MDFF_NM with other existing methods and integrative modeling pipelines is also discussed.

Cholesterol transfer to high-density lipoprotein in obesity and the effects of weight loss after bariatric surgery.

Obesity increases serum triglycerides and decreases high-density lipoprotein cholesterol (HDL-C). The objective is to explore some functions of HDL, cholesterol transfers and antioxidant, in subjects with grade I (G1-OB) and III (G3-OB) obesity and effects of bariatric surgery on G3-OB. Fifteen G3-OB patients (43 ± 6 years, BMI 49 ± 3 kg/m2) were studied before and 1 year after bariatric surgery; 15 G1-OB (32 ± 2 years, 32 ± 2 kg/m2) and 15 normal weight (NW) (38 ± 6 years, 22 ± 1 kg/m2) were also studied. HDL diameter, cholesterol transfer to HDL and antioxidant capacity of HDL were determined. G3-OB had higher triglycerides and lower HDL-C; G1-OB had higher triglycerides than NW but HDL-C was equal. Compared to NW, HDL size was smaller in G3-OB but equal in G1-OB. One year after bariatric surgery, BMI and triglycerides of G3-OB decreased (p < .0001 and p = .0012, respectively) and HDL-C increased (p < .0001), equalling of NW group. Antioxidant capacity and cholesterol transfers were not different in groups and were unchanged 1 year after bariatric surgery in G3-OB. HDL antioxidant capacity and transfer of cholesterol to HDL were not defective in obesity despite HDL-C reduction and smaller HDL size. In addition, pronounced weight loss by bariatric surgery did not change those protective functions.

Microbial successional pattern along a glacier retreat gradient from Byers Peninsula, Maritime Antarctica.

The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied 14C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.

Current Challenges and Perspectives in Breast Cancer in Elderly Women: The Senologic International Society (SIS) Survey.

Objective: Mammographic screening and management of breast cancer (BC) in elderly women are controversial and continue to be an important health problem. To investigate, through members of the Senologic International Society (SIS), the current global practices in BC in elderly women, highlighting topics of debate and suggesting perspectives. Materials and Methods: The questionnaire was sent to the SIS network and included 55 questions on definitions of an elderly woman, BC epidemiology, screening, clinical and pathological characteristics, therapeutic management in elderly women, onco-geriatric assessment and perspectives. Results: Twenty-eight respondents from 21 countries and six continents, representing a population of 2.86 billion, completed and submitted the survey. Most respondents considered women 70 years and older to be elderly. In most countries, BC was often diagnosed at an advanced stage compared to younger women, and age-related mortality was high. For this reason, participants recommended that personalized screening be continued in elderly women with a long life expectancy.In addition, this survey highlighted that geriatric frailty assessment tools and comprehensive geriatric evaluations needed to be used more and should be developed to avoid undertreatment. Similarly, multidisciplinary meetings dedicated to elderly women with BC should be encouraged to avoid under- and over-treatment and to increase their participation in clinical trials. Conclusion: Due to increased life expectancy, BC in elderly women will become a more important field in public health. Therefore, screening, personalized treatment, and comprehensive geriatric assessment should be the cornerstones of future practice to avoid the current excess of age-related mortality. This survey described, through members of the SIS, a global picture of current international practices in BC in elderly women.

Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus.

The mutualistic ectomycorrhizal (ECM) fungal genus Pisolithus comprises 19 species defined to date which colonize the roots of >50 hosts worldwide suggesting that substantial genomic and functional evolution occurred during speciation. To better understand this intra-genus variation, we undertook a comparative multi-omic study of nine Pisolithus species sampled from North America, South America, Asia, and Australasia. We found that there was a small core set of genes common to all species (13%), and that these genes were more likely to be significantly regulated during symbiosis with a host than accessory or species-specific genes. Thus, the genetic "toolbox" foundational to the symbiotic lifestyle in this genus is small. Transposable elements were located significantly closer to gene classes including effector-like small secreted proteins (SSPs). Poorly conserved SSPs were more likely to be induced by symbiosis, suggesting that they may be a class of protein that tune host specificity. The Pisolithus gene repertoire is characterized by divergent CAZyme profiles when compared with other fungi, both symbiotic and saprotrophic. This was driven by differences in enzymes associated with symbiotic sugar processing, although metabolomic analysis suggest that neither copy number nor expression of these genes is sufficient to predict sugar capture from a host plant or its metabolism in fungal hyphae. Our results demonstrate that intra-genus genomic and functional diversity within ECM fungi is greater than previously thought, underlining the importance of continued comparative studies within the fungal tree of life to refine our focus on pathways and evolutionary processes foundational to this symbiotic lifestyle.

MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments.

Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions. Herein, we developed a new automated open-source implementation, MDexciteR (https://github.com/mcosta27/MDexciteR), enabling the integration of MDeNM with two commonly used simulation programs with GPU support. Second, we generalized the method to include the excitation of principal components calculated from experimental ensembles. Finally, we evaluated whether the use of coarse-grained normal modes calculated with elastic network representations preserved the performance and accuracy of the method. The advantages and limitations of these new approaches are discussed based on results obtained for three different protein test cases: two globular and a protein/membrane system.

Fatores associados ao baixo apgar em recém-nascidos angolanos / Factors associated with low apgar in angolan newborn / Factores asociados con apgar bajo en recién nacidos angolanos

Objetivo:avaliar os fatores associados ao baixo Apgar em recém-nascidos de Angola. Método:estudo analíticoe transversal, quali-quantitativo, em umHospital Geral de Luanda, Angola, entre março e maio de 2021. Realizou-se entrevistas em sala de observação e consulta aos prontuários das parturientes. Os dados foram analisados pelo teste qui-quadrado (X2) e regressão logística. Resultados:prevaleceu parturientes entre 19-35 anos (70,0%), 7º-9º ano (57,5%), multíparas (75%), multigestas (75,0%), sem histórico de aborto (72,5%), idade gestacional de 40 semanas (60,0%), usuárias de bebidas alcoólicas (77,5%), baixa frequência de consultas pré-natais (52,5%), com parto natural (82,5%) e recém-nascidos com peso normal (52,5%). Mulheres de região periurbana [OR:6,85 (95% CI:0.65-71,2), p=0,108] e rural [OR:4,47 (95% CI:0.47-48,4), p=0,184] apresentaram maior chance de terem recém-nascidos com baixo Apgar, assim como as usuárias de álcool [OR:3,28 (95% CI:0,58-18,3), p=0,176] e recém-nascidos que nasceram com peso normal [OR:1,75 (95% CI:0,49­6,22), p=0,387]. Não houve associação estatística entre os dados sociodemográficos e maternos. Conclusão:a faixa etária, local de residência, consumo de álcool materno e peso do recém-nascido podem implicar em baixo Apgar.

Objective: to evaluate the factors associated with low Apgar in newborns in Angola. Method:analytical and cross-sectional, quali-quantitative study, in a General Hospital in Luanda, Angola, between March and May 2021. Interviews were carried out in an observation room and consultation of the parturients' medical records. Data were analyzed using the chi-square test (X2) and logistic regression.Results: pregnant women aged 19-35 years (70.0%), 7th-9th year(57.5%), multiparous (75%), multiparous (75.0%), without a history of abortion (72.5%), prevailed. gestational age of 40 weeks (60.0%), users of alcoholic beverages (77.5%), low frequency of prenatal consultations (52.5%), with natural childbirth (82.5%) and newborns with normal weight (52.5%). Women from peri-urban regions [OR:6.85 (95% CI:0.65-71.2), p=0.108] and rural [OR:4.47 (95% CI:0.47-48.4), p=0.184] were more likely to have low Apgar newborns, as well as alcohol users [OR:3.28 (95% CI:0.58-18.3), p=0.176] and newborns who were born with normal [OR:1.75 (95% CI:0.49­6.22), p=0.387]. There was no statistical association between sociodemographic and maternal data.Conclusion: age group, place of residence, maternal alcohol consumption and newborn weight may imply low Apgar.

Objetivo: evaluar los factores asociados al Apgar bajo en recién nacidos en Angola.Método: estudio analítico y transversal, cuali-cuantitativo, en un Hospital General de Luanda, Angola, entre marzo y mayo de 2021. Se realizaron entrevistas en sala de observación y consulta de las historias clínicas de las parturientas. Los datos se analizaron mediante la prueba de chi-cuadrado (X2) y regresión logística. Resultados: gestantes de 19 a 35 años (70,0%), de 7° a 9° año (57,5%), multíparas (75%), multíparas (75,0%), sin antecedente de aborto (72,5%), predominó la edad gestacional de 40 semanas (60,0%), usuarias de bebidas alcohólicas (77,5%), baja frecuencia de consultas prenatales (52,5%), con parto natural (82,5%) y recién nacidos con normopeso (52,5%). Las mujeres de regiones periurbanas [OR:6,85 (IC 95%:0,65-71,2), p=0,108] y rurales [OR:4,47 (IC 95%:0,47-48,4), p=0,184] tenían más probabilidades de tener bajo Recién nacidos Apgar, así como consumidores de alcohol [OR:3,28 (IC 95%:0,58-18,3), p=0,176] y recién nacidos que nacieron con normalidad [OR:1,75 (IC 95%:0,49-6,22), p=0,387]. No hubo asociación estadística entre datos sociodemográficos y maternos. Conclusión: el grupo de edad, el lugar de residencia, el consumo materno de alcohol y el peso del recién nacido pueden implicar un Apgar bajo.

Possible Amazonian contribution to Sargassum enhancement on the Amazon Continental Shelf.

The Amazon Continental Shelf (ACS) has a coastline of ∼1000 km and is situated in a humid equatorial region with two distinct seasons, wet and dry, and two transitional climatic periods. A total of eight oceanographic cruises were conducted to investigate the dynamics of the inorganic nutrients dissolved in the surface layer of the water column of the ACS and their associations with Sargassum blooms. An excess of nitrogen-N* (NH4+ = 0.01-9.30 µmol l-1) was verified through the salinity gradient from the continent to the ACS, mainly during the period of maximum discharge of the Amazon and Tocantins-Pará rivers. The highest NH4+ concentrations coincided with the occurrence of macrophyte (Sargassum sp.) blooms in the mesohaline and oceanic regions. During this period the high values of NH4+ accompany the low values of Sea Surface Salinity (SSS), indicating the advection of the Amazonian plume towards the Caribbean Sea. In the Sargassum belts we observed a N:P ratio = 60:1 during wet period, while outside this region, the N:P ratio was 34:1. According to DIN vs. AOU ratio, we observed that heterotrophic processes prevail over productive processes, mainly in the mesohaline and low salinity regions. Nitrogen concentrations from runoff, mainly from hydrographic basins, showed significant increases in the last decade, mainly due to anthropogenic factors such as agriculture, deforestation, livestock, urban sewage (domestic and industrial), and demographic growth of the population in the Tocantins-Pará Basin. Additionally, associations of diatoms and cyanobacteria provide more nitrogen in the mesohaline and oceanic regions that nourishes Sargassum blooms. Seasonal comparisons (October and April) of Sargassum belts with other studies, indicated that currents play a fundamental role in the transport of these macrophytes from the east edge (Africa) to the west edge (Brazil and French Guiana) towards the Caribbean Sea in the tropical Atlantic.

The Senologic International Society Survey on Ductal Carcinoma In Situ: Present and Future.

Objective: Therapeutic management of ductal carcinoma in situ (DCIS) is heterogeneous among countries worldwide, and some treatment indications are still controversial. To investigate DCIS management in different countries; identify both consensual practices and controversial topics; and survey opinions about the future management of DCIS. Materials and Methods: The Senologic International Society network members participated to an online survey using a questionnaire, between November 2021 and February 2022. Results: Twenty-two responses from 20 different countries showed that organized breast cancer screening programs were present for 87% participants, and DCIS cases represented 13.7% of all breast cancers. Most participants used the grade classification (100%), the morphological classification (78%) and performed immunohistochemistry assays (73%). In case of conservative treatment, the mean re-excision rate was 10.3% and clear margins of mean 2.5 mm were considered healthy. Radical mastectomy rate was 35.5% with a breast reconstruction rate of 53%. Tumor bed boost indications were heterogeneous, and 73% of participants indicated hormone therapy for hormone-positive DCIS. Surgery and radiotherapy omission for some low-risk DCIS were considered by 73% of participants. Multigene assays were used by 43% of participants. Concerning future changes in DCIS management, participants mostly answered surgical de-escalation (48%), radiotherapy de-escalation (35) and/or active surveillance for some cases (22%). Conclusion: This survey provided an overview of the current practices of DCIS management worldwide. It showed that some areas are rather consensual: incidence increases over time, treatment in young women, pathological classifications, definition of healthy margins, the skin-sparing mastectomy and immediate breast reconstruction. However, some topics are still debated and result in heterogeneous practices, such as evolution in the age of diagnosis, the benefit of de-escalation in low-risk DCIS among elderly women, indications for hormone therapy, radiotherapy omission, or multigene assays. Further evidence is needed to reach consensus on these points, and innovative approaches are still under evaluation in clinical trials. The International Senologic Society, by its members, encourages precision medicine and personalized treatments for DCIS, to avoid overtreatment and overdiagnosis, and provide better healthcare to women with DCIS.

The C-Terminal Acidic Tail Modulates the Anticancer Properties of HMGB1.

Energy metabolism reprogramming was recently listed as a hallmark of cancer. In this process, the switch from pyruvate kinase isoenzyme type M1 to pyruvate kinase isoenzyme type M2 (PKM2) is believed to play a crucial role. Interestingly, the activity of the active form of PKM2 can efficiently be inhibited by the high-mobility group box 1 (HMGB1) protein, leading to a rapid blockage of glucose-dependent aerobic respiration and cancer cell death. HMGB1 is a member of the HMG protein family. It contains two DNA-binding HMG-box domains and an acidic C-terminal tail capable of positively or negatively modulating its biological properties. In this work, we report that the deletion of the C-terminal tail of HMGB1 increases its activity towards a large panel of cancer cells without affecting the viability of normal immortalized fibroblasts. Moreover, in silico analysis suggests that the truncated form of HMGB1 retains the capacity of the full-length protein to interact with PKM2. However, based on the capacity of the cells to circumvent oxidative phosphorylation inhibition, we were able to identify either a cytotoxic or cytostatic effect of the proteins. Together, our study provides new insights in the characterization of the anticancer activity of HMGB1.