Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing

Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM-encapsulating, stably-inverted apical-out human upper airway organoids (AORBs) that are large (~500 μm diameter), consistently spherical, recapitulate in vivo-like cellular heterogeneity, and maintain their inverted morphology for over 60 days. Treatment of AORBs with IL-13 skews differentiation towards goblet cells and the apical-out geometry allows extra-organoid mucus collection. AORB maturation for 14 days induces strong co-expression of ACE2 and TMPRSS2 to allow high-yield infection with five SARS-CoV-2 variants. Dose-response analysis of three well-studied SARS-CoV-2 antiviral compounds [remdesivir, bemnifosbuvir (AT-511), and nirmatrelvir] shows AORB antiviral assays to be comparable to gold-standard air-liquid interface cultures, but with higher throughput (~10-fold) and fewer cells (~100-fold). While this work focuses on SARS-CoV-2 applications, the consistent AORB shape and size, and one-organoid-per-well modularity broadly impacts in vitro human cell model standardization efforts in line with economic imperatives and recently updated FDA regulation on therapeutic testing.

Mechanisms by which the cystic fibrosis transmembrane conductance regulator may influence SARS-CoV-2 infection and COVID-19 disease severity

Patients with cystic fibrosis (CF) exhibit pronounced respiratory damage and were initially considered among those at highest risk for serious harm from SARS-CoV-2 infection. Numerous clinical studies have subsequently reported that individuals with CF in North America and Europe-while susceptible to severe COVID-19-are often spared from the highest levels of virus-associated mortality. To understand features that might influence COVID-19 among patients with cystic fibrosis, we studied relationships between SARS-CoV-2 and the gene responsible for CF (i.e., the cystic fibrosis transmembrane conductance regulator, CFTR). In contrast to previous reports, we found no association between CFTR carrier status (mutation heterozygosity) and more severe COVID-19 clinical outcomes. We did observe an unexpected trend toward higher mortality among control individuals compared with silent carriers of the common F508del CFTR variant-a finding that will require further study. We next performed experiments to test the influence of homozygous CFTR deficiency on viral propagation and showed that SARS-CoV-2 production in primary airway cells was not altered by the absence of functional CFTR using two independent protocols. On the contrary, experiments performed in vitro strongly indicated that virus proliferation depended on features of the mucosal fluid layer known to be disrupted by absent CFTR in patients with CF, including both low pH and increased viscosity. These results point to the acidic, viscous, and mucus-obstructed airways in patients with cystic fibrosis as unfavorable for the establishment of coronaviral infection. Our findings provide new and important information concerning relationships between the CF clinical phenotype and severity of COVID-19.

A Novel 7H-[1,2,4]Triazolo[3,4-b]thiadiazine-based Cystic Fibrosis Transmembrane Conductance Regulator Potentiator Directed toward Treatment of Cystic Fibrosis

Cystic fibrosis (CF) is an autosomal genetic disorder caused by disrupted anion transport in epithelial cells lining tissues in the human airways and digestive system. While cystic fibrosis transmembrane conductance regulator (CFTR) modulator compounds have provided transformative improvement in CF respiratory function, certain patients exhibit marginal clinical benefit or detrimental effects or have a form of the disease not approved or unlikely to respond using CFTR modulation. We tested hit compounds from a 300,000-drug screen for their ability to augment CFTR transepithelial transport alone or in combination with the FDA-approved CFTR potentiator ivacaftor (VX-770). A subsequent SAR campaign led us to a class of 7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazines that in combination with VX-770 rescued function of G551D mutant CFTR channels to approximately 400% above the activity of VX-770 alone and to nearly wild-type CFTR levels in the same Fischer rat thyroid model system.

Engineered tRNAs suppress nonsense mutations in cells and in vivo

Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into  efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.

Selective biosorption of lanthanides onto Galdieria sulphuraria

The recovering of trivalent Lanthanides from aqueous solutions, by biosorption process onto Galdieria sulphuraria lifeless cells, was investigated. Potentiometry, UV-Vis, FTIR-ATR spectroscopy and SEM-EDS analysis were used. All the experiments were performed at 25 °C, in 0.5 M NaCl. Ln³⁺ biosorption is greater in the 5-6 pH range with values ranging from 80 μmol/g to 130 μmol/g (dry weight). The adsorbed Ln³⁺ ions can be recovered at higher acidity (pH<1) and the biosorbent can be reused. Specific molecular interactions between Ln³⁺ ions and the functional groups on G. sulphuraria surface were highlighted. Particularly, proteins are involved if Ln³⁺=Pr³⁺, Sm³⁺, Eu³⁺, Tb³⁺, Dy³⁺, Tm³⁺, while Ce³⁺, Ho³⁺, Er³⁺ form bonds with carbohydrates. Finally, both proteins and carbohydrates are involved if Gd³⁺ and Yb³⁺. A Surface Complexation approach, with a good graphical fitting to potentiometric experimental collected data, was used to describe the biosorption mechanism. This study could be of great applicative utility for removing of trivalent actinides, from waste aqueous solutions, by biosorption. As well known the lanthanides were used as model to simulate the chemical behaviour of actinides in the same oxidation state.

Speaking with mask in the COVID-19 era: Multiclass machine learning classification of acoustic and perceptual parameters

The intensive use of personal protective equipment often requires increasing voice intensity, with possible development of voice disorders. This paper exploits machine learning approaches to investigate the impact of different types of masks on sustained vowels /a/, /i/, and /u/ and the sequence /a'jw/ inside a standardized sentence. Both objective acoustical parameters and subjective ratings were used for statistical analysis, multiple comparisons, and in multivariate machine learning classification experiments. Significant differences were found between mask+shield configuration and no-mask and between mask and mask+shield conditions. Power spectral density decreases with statistical significance above 1.5 kHz when wearing masks. Subjective ratings confirmed increasing discomfort from no-mask condition to protective masks and shield. Machine learning techniques proved that masks alter voice production: in a multiclass experiment, random forest (RF) models were able to distinguish amongst seven masks conditions with up to 94% validation accuracy, separating masked from unmasked conditions with up to 100% validation accuracy and detecting the shield presence with up to 86% validation accuracy. Moreover, an RF classifier allowed distinguishing male from female subject in masked conditions with 100% validation accuracy. Combining acoustic and perceptual analysis represents a robust approach to characterize masks configurations and quantify the corresponding level of discomfort.

Marine Natural Products as Leads against SARS-CoV-2 Infection

Since early 2020, disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic, causing millions of infections and deaths worldwide. Despite rapid deployment of effective vaccines, it is apparent that the global community lacks multipronged interventions to combat viral infection and disease. A major limitation is the paucity of antiviral drug options representing diverse molecular scaffolds and mechanisms of action. Here we report the antiviral activities of three distinct marine natural products─homofascaplysin A (1), (+)-aureol (2), and bromophycolide A (3)─evidenced by their ability to inhibit SARS-CoV-2 replication at concentrations that are nontoxic toward human airway epithelial cells. These compounds stand as promising candidates for further exploration toward the discovery of novel drug leads against SARS-CoV-2.

Are insulin resistance and non-alcoholic fatty liver disease associated with Peyronie's disease? A pilot study

Risk factors for Peyronie's disease (PD) are serum lipid abnormalities, hypertension and type 2 diabetes mellitus (T2DM). Oxidative stress and inflammation are key-players in the pathogenesis of arterial diseases, leading to insulin resistance (IR), which is a major determinant of non-alcoholic fatty liver disease (NAFLD). We studied the potential relationship between PD, IR, and NAFLD. Forty-nine male patients were enrolled, fulfilling the well-accepted diagnostic criteria of stable PD. Fifty male individuals without PD, well-matched for age and BMI, were selected as the control group. Comorbidities (T2DM and hypertension), as well as the lipid profile and the glucometabolic asset, were evaluated. The triglycerides/HDL ratio (TG/HDL-C ratio) with a cut-off of ≥3 and the triglycerides-glucose index (TyG) with an optimal cut-point of 8.5 were used for diagnosis of IR and NAFLD, respectively. NAFLD diagnosis was confirmed by the presence of bright liver at ultrasonography. Hypertension was found more frequently in PD patients than in no-PD subjects (P=0.017), independently of age (P=0.99). Both IR and NAFLD were significantly associated with the presence of PD in our population of men (P=0.043 and 0.0001, respectively), no matter how old (P=0.11 and 0.74, respectively). At logistic regression, NAFLD was the only predictor of the PD presence (p=0.021). The AUROC of TyG to predict PD was 0.7437 (sensitivity 67.35% and specificity 80%) with a percentage of correctly classified patients of 73.74%. Oxidative stress markers were significantly associated with NAFLD. Testosterone level was significantly low in the subjects with NAFLD in cross-sectional analyses. Both factors, i.e., oxidative stress and hypogonadism, are central to PD pathogenesis. In conclusion, NAFLD and IR are strongly associated with PD. The pathogenic link between these conditions and the underlying mechanisms are only hypothetical and thoroughly summarized in the discussion.

A medium composition containing normal resting glucose that supports differentiation of primary human airway cells

Primary cells isolated from the human respiratory tract are the state-of-the-art for in vitro airway epithelial cell research. Airway cell isolates require media that support expansion of cells in a basal state to maintain the capacity for differentiation as well as proper cellular function. By contrast, airway cell differentiation at an air-liquid interface (ALI) requires a distinct medium formulation that typically contains high levels of glucose. Here, we expanded and differentiated human basal cells isolated from the nasal and conducting airway to a mature mucociliary epithelial cell layer at ALI using a medium formulation containing normal resting glucose levels. Of note, bronchial epithelial cells expanded and differentiated in normal resting glucose medium showed insulin-stimulated glucose uptake which was inhibited by high glucose concentrations. Normal glucose containing ALI also enabled differentiation of nasal and tracheal cells that showed comparable electrophysiological profiles when assessed for cystic fibrosis transmembrane conductance regulator (CFTR) function and that remained responsive for up to 7 weeks in culture. These data demonstrate that normal glucose containing medium supports differentiation of primary nasal and lung epithelial cells at ALI, is well suited for metabolic studies, and avoids pitfalls associated with exposure to high glucose.

[Impact of COVID-19 outbreak on urology surgical waiting lists and waiting lists prioritization strategies in the Post-COVID-19 era]

Introduction

The suspension of most elective surgeries during COVID-19 pandemic caused the lengthening of urology surgical waiting lists. The objective of this study is to evaluate the impact of COVID-19 pandemic on urology surgical waiting list in a high-volume hospital.

Methods

An observational descriptive study was designed. All patients included in the urology surgical waiting list of our high-volume center on May 1st 2020 (46 days after the suspension of elective surgery) were analyzed. Baseline variables, priority on the waiting list, main urological disease, type of scheduled surgery, and waiting time were recorded. Other variables recorded were the presence of a urinary catheter, number of accesses to the emergency department, evidence of COVID-19 infection, number of deaths and their cause. The waiting time for each disease was compared with the time to surgery in 2019.

Results

A total of 350 patients were included. The mean (SD) time on the waiting list was 97.33 (55.47) days. Priority 1 patients, who normally should undergo surgery within 30 days, were on the waiting list for a mean (SD) time of 60.51 (20.14) days. They were mainly patients with ureteral lithiasis (25.6%), high-risk or muscle-invasive bladder cancer (20.9%) and high-risk prostate cancer (13.9%). The mean waiting time had already significantly exceeded the mean time to surgery in 2019 for radical cystectomy (p = 0.04) and URS (p = 0.003).

Conclusions

The suspension of most elective surgeries due to COVID-19 had a significant impact on urology surgical waiting list of our high-volume center, especially in priority 1 group.

Bacillus subtilis PcrA Couples DNA Replication, Transcription, Recombination and Segregation

Bacillus subtilis PcrA abrogates replication-transcription conflicts in vivo and disrupts RecA nucleoprotein filaments in vitro. Inactivation of pcrA is lethal. We show that PcrA depletion lethality is suppressed by recJ (involved in end resection), recA (the recombinase), or mfd (transcription-coupled repair) inactivation, but not by inactivating end resection (addAB or recQ), positive and negative RecA modulators (rarA or recX and recU), or genes involved in the reactivation of a stalled RNA polymerase (recD2, helD, hepA, and ywqA). We also report that B. subtilis mutations previously designated as recL16 actually map to the recO locus, and confirm that PcrA depletion lethality is suppressed by recO inactivation. The pcrA gene is epistatic to recA or mfd, but it is not epistatic to addAB, recJ, recQ, recO16, rarA, recX, recU, recD2, helD, hepA, or ywqA in response to DNA damage. PcrA depletion led to the accumulation of unsegregated chromosomes, and this defect is increased by recQ, rarA, or recU inactivation. We propose that PcrA, which is crucial to maintain cell viability, is involved in different DNA transactions.

Phonetic analysis during treatment with rapid maxillary expander

OBJECTIVES

To investigate possible changes and/or device-related impairments in phonetic habits produced by rapid maxillary expansion (RME).

MATERIALS AND METHODS

Thirty-five patients scheduled for RME were divided into two groups: Group A (banded two-arm Hyrax) and Group B (banded four-arm Hyrax). Speech samples were collected at six time points, before, during and after RME removal. Acoustical analysis was performed using PRAAT and BioVoice analysis tools. Ten volunteers completed a questionnaire on the acceptability of patient's speech. Maxillary dimensions and palatal volume were measured on dental casts before and after expansion using a digital gauge.

RESULTS

Voice analysis showed an increase in the peak frequency of fricative consonants (/s/,/ʃ/) after expansion, whereas there was no change of formant frequencies of palatal consonants (/ɲ/,/ʎ/). Vowel /i/ displayed a lowering of the first formant frequency, and an increase in the second and third formant frequencies. After bonding, Group B showed both a greater reduction in the peak frequency of fricatives and a greater increase in the formant frequencies of palatal consonants than Group A.

CONCLUSION

Rapid maxillary expansion causes a slight phonetic change in the acoustical parameters of both consonants and vowels. The two-arm Hyrax caused less speech impairment than the four-arm Hyrax during the treatment.

Laparoscopic pancreatectomy: Did the indications change? A review from literature

Pancreatic Cancer (PC) is the fourth cause of death for tumors in Western countries. Symptoms are not specific, and can vary according to the tumor size and place. Diagnostic workup includes CA 19-9, CT and MRI. Surgery is the only treatment for PC, associated to radio-chemo therapy. Laparoscopic approaches are actually used for PC treatment in few specialized centers, and could be an alternative to laparotomic surgery. The aim of our study is to evaluate the efficacy of laparoscopy for PC treatment compared to laparotomy. We reviewed 19 articles in literature to assess the feasibility and efficacy of Laparoscopic Distal Pancreatectomy (LDP) and Laparoscopic Pancreaticoduodenectomy (LPD). The results have shown that LDP is nowadays a safe technique, and the outcomes are comparable to laparotomic surgery. Regarding to LPD instead, results are controversial and the data are still not sufficient to consider this technique as a valid alternative to laparotomic surgery.

Chemical immobilisation of free-ranging Pampas foxes (Pseudalopex gymnocercus): Assessment of ketamine-xylazine and tiletamine-zolazepam combinations

Two protocols to immobilise free-ranging Pampas foxes for ear-tagging or radio-collaring were evaluated. One hundred fifteen foxes were injected with ketamine-xylazine (K-X) and thirteen with tiletamine-zolazepam (T-Z). The use of both T-Z and K-X combinations typically resulted in a smooth induction and recovery. In 86% of the cases K-X protocol was judged effective (mean±SD, K: 10.7±3.3mg/kg, X: 1.0±1.0mg/kg) while T-Z protocol was judged effective in 92% of the cases (T: 3.6±1.05mg/kg, Z: 3.6±1.05mg/kg). The primary differences between the two drug combinations were that the time necessary for the complete recovery was longer with T-Z, and thermic problems were found more frequently with K-X. Additionally, our results suggest that thermic stress may be a relatively frequent complication for Pampas foxes. This study provides baseline data on some physiologic variables in Pampas foxes captured with different methods and drugs in field conditions.

Automatic newborn cry analysis: a non-invasive tool to help autism early diagnosis

Autism Spectrum Disorders (ASD) are complex developmental disabilities that cause problems with social interaction and communication. ASD are associated with motor development problems, more or less blurred, and with perceptual and sensory brain areas. Crying is the infant's earliest form of communication and recent studies connect this original "language" form with autism disturbs. Being completely non-invasive, cry analysis is an appealing approach for early ASD diagnosis to improve rehabilitation. To this aim, we have developed an automatic system to record newborn cry and movements, during the first six months of life with a specific recording protocol. In this work we present first results of acoustic cry analysis in newborns classified as high-risk subjects being siblings of children already diagnosed as autistics. The work aims at finding possible early ASD signs in high-risk subjects as compared to a group of control subjects based on the fundamental frequency and the vocal tract resonance frequencies. Also, voiced and unvoiced parts of signal and cry-episodes duration are analyzed.

Voicing quantification is more relevant than period perturbation in substitution voices: an advanced acoustical study

Quality of substitution voicing—i.e., phonation with a voice that is not generated by the vibration of two vocal folds—cannot be adequately evaluated with routinely used software for acoustic voice analysis that is aimed at ‘common’ dysphonias and nearly periodic voice signals. The AMPEX analysis program (Van Immerseel and Martens) has been shown previously to be able to detect periodicity in irregular signals with background noise, and to be suited for running speech. The validity of this analysis program is first tested using realistic synthesized voice signals with known levels of cycle-to-cycle perturbations and additive noise. Second, exhaustive acoustic analysis is performed of the voices of 116 patients surgically treated for advanced laryngeal cancer and recorded in seven European academic centers. All of them read out a short phonetically balanced passage. Patients were divided into six groups according to the oscillating structures they used to phonate. Results show that features related to quantification of voicing enable a distinction between the different groups, while the features reporting F₀-instability fail to do so. Acoustic evaluation of voice quality in substitution voices thus best relies upon voicing quantification.

Impact of the new european paediatric regulatory framework on ethics committees: overview and perspectives

AIM

To evaluate the impact of the new European paediatric regulatory framework on the activities of Ethics Committees operating in Europe and to assess their involvement and interest in paediatric research.

METHODS

Task-force in Europe for Drug Development for the Young Network of Excellence and Relating Expectations and Needs to the Participation and Empowerment of Children in Clinical Trials project set up an inventory of Ethics Committees existing in Europe and conducted a survey on their approach to paediatric trials.

RESULTS

Ethics Committees operating in 22 European Countries participated in this survey. Results showed a high lack of knowledge, understanding and awareness of the current European paediatric regulatory framework and a lack of involvement of Ethics Committees in paediatric research, especially in terms of training and education, demonstrated also by the decreasing number of Ethics Committees answering exhaustively to the whole questionnaire. The majority of participating Ethics Committees expressed interest in future initiatives related to paediatric research.

CONCLUSIONS

Despite a limited knowledge and understanding of the current paediatric regulatory framework, a significant number of Ethics Committees operating in Europe show interest in initiatives related to paediatric research. Networking may be an essential tool to be used to enhance Ethics Committees role in supporting paediatric research. Any initiative should be undertaken at European level in collaboration with European Union Institutions.

Tridimensional assessment of adductor spasmodic dysphonia pre- and post-treatment with Botulinum toxin

Spasmodic dysphonia voices form, in the same way as substitution voices, a particular category of dysphonia that seems not suited for a standardized basic multidimensional assessment protocol, like the one proposed by the European Laryngological Society. Thirty-three exhaustive analyses were performed on voices of 19 patients diagnosed with adductor spasmodic dysphonia (SD), before and after treatment with Botulinum toxin. The speech material consisted of 40 short sentences phonetically selected for constant voicing. Seven perceptual parameters (traditional and dedicated) were blindly rated by a panel of experienced clinicians. Nine acoustic measures (mainly based on voicing evidence and periodicity) were achieved by a special analysis program suited for strongly irregular signals and validated with synthesized deviant voices. Patients also filled in a VHI-questionnaire. Significant improvement is shown by all three approaches. The traditional GRB perceptual parameters appear to be adequate for these patients. Conversely, the special acoustic analysis program is successful in objectivating the improved regularity of vocal fold vibration: the basic jitter remains the most valuable parameter, when reliably quantified. The VHI is well suited for the voice-related quality of life. Nevertheless, when considering pre-therapy and post-therapy changes, the current study illustrates a complete lack of correlation between the perceptual, acoustic, and self-assessment dimensions. Assessment of SD-voices needs to be tridimensional.

Spatial organization of Molina’s hog-nosed skunk (Conepatus chinga) in two landscapes of the Pampas grassland of Argentina

We radio-tracked 16 individuals (6 males, 10 females) of the little known Molina’s hog-nosed skunk ( Conepatus chinga (Molina, 1782)) and compared home-range dynamics, movement rates, and densities between a protected area and a landscape fragmented by agriculture. The mean home-range size (95% fixed kernel) was 166.7 ha (SD = 107.5 ha), without significant differences between areas. Home-range size varied significantly between males (mean = 243.7 ha, SD = 76.5 ha) and females (mean = 120.4 ha, SD =77.6 ha). Overlap between home range and core area was extensive between and within sexes in the protected area and more limited in the cropland area. Mean distance traveled between two consecutive resting sites was 269.5 m (SD = 365 m) and did not differ between areas, although movements were greater for males than females. Distance moved was influenced by seasons, being greater during the cold period. Finally, density estimates were consistently greater at the protected area. We argue that home-range size in Molina’s hog-nosed skunks is an inherent species property, whereas population density and territoriality are more flexible parameters that could reflect how the ecosystem state was affected. In our study, the greater dispersion of food patches in the cropland area than in the protected area may be the major factor influencing these parameters.

In vitro studies of DNA mismatch repair proteins

The ability to monitor and characterize DNA mismatch repair activity in various mammalian cells is important for understanding mechanisms involved in mutagenesis and tumorigenesis. Since mismatch repair proteins recognize mismatches containing both normal and chemically altered or damaged bases, in vitro assays must accommodate a variety of mismatches in different sequence contexts. Here we describe the construction of DNA mismatch substrates containing G:T or O(6)meG:T mismatches, the purification of recombinant native human MutSα (MSH2-MSH6) and MutLα (MLH1-PMS2) proteins, and in vitro mismatch repair and excision assays that can be adapted to study mismatch repair in nuclear extracts from mismatch repair proficient and deficient cells.

RecO-mediated DNA homology search and annealing is facilitated by SsbA

Bacillus subtilis RecO plays a central role in recombinational repair and genetic recombination by (i) stimulating RecA filamentation onto SsbA-coated single-stranded (ss) DNA, (ii) modulating the extent of RecA-mediated DNA strand exchange and (iii) promoting annealing of complementary DNA strands. Here, we report that RecO-mediated strand annealing is facilitated by cognate SsbA, but not by a heterologous one. Analysis of non-productive intermediates reveals that RecO interacts with SsbA-coated ssDNA, resulting in transient ternary complexes. The self-interaction of ternary complexes via RecO led to the formation of large nucleoprotein complexes. In the presence of homology, SsbA, at the nucleoprotein, removes DNA secondary structures, inhibits spontaneous strand annealing and facilitates RecO loading onto SsbA–ssDNA complex. RecO relieves SsbA inhibition of strand annealing and facilitates transient and random interactions between homologous naked ssDNA molecules. Finally, both proteins lose affinity for duplex DNA. Our results provide a mechanistic framework for rationalizing protein release and dsDNA zippering as coordinated events that are crucial for RecA-independent plasmid transformation.

Evidence for different pathways during horizontal gene transfer in competent Bacillus subtilis cells

Cytological and genetic evidence suggests that the Bacillus subtilis DNA uptake machinery localizes at a single cell pole and takes up single-stranded (ss) DNA. The integration of homologous donor DNA into the recipient chromosome requires RecA, while plasmid establishment, which is independent of RecA, requires at least RecO and RecU. RecA and RecN colocalize at the polar DNA uptake machinery, from which RecA forms filamentous structures, termed threads, in the presence of chromosomal DNA. We show that the transformation of chromosomal and of plasmid DNA follows distinct pathways. In the absence of DNA, RecU accumulated at a single cell pole in competent cells, dependent on RecA. Upon addition of any kind of DNA, RecA formed highly dynamic thread structures, which rapidly grew and shrank, and RecU dissipated from the pole. RecO visibly accumulated at the cell pole only upon addition of plasmid DNA, and, to a lesser degree, of phage DNA, but not of chromosomal DNA. RecO accumulation was weakly influenced by RecN, but not by RecA. RecO annealed ssDNA complexed with SsbA in vitro, independent of any nucleotide cofactor. The DNA end-joining Ku protein was also found to play a role in viral and plasmid transformation. On the other hand, transfection with SPP1 phage DNA required functions from both chromosomal and plasmid transformation pathways. The findings show that competent bacterial cells possess a dynamic DNA recombination machinery that responds in a differential manner depending if entering DNA shows homology with recipient DNA or has self-annealing potential. Transformation with chromosomal DNA only requires RecA, which forms dynamic filamentous structures that may mediate homology search and DNA strand invasion. Establishment of circular plasmid DNA requires accumulation of RecO at the competence pole, most likely mediating single-strand annealing, and RecU, which possibly down-regulates RecA. Transfection with SPP1 viral DNA follows an intermediate route that contains functions from both chromosomal and plasmid transformation pathways.

Many bacteria can actively acquire novel genetic material from their environment, which leads to the rapid spreading of, for example, antibiotic resistance genes. The bacterium Bacillus subtilis can differentiate into the state of competence, in which cells take up ssDNA through a DNA uptake complex that is specifically localized at a single cell pole. DNA can be integrated into the chromosome, via RecA, or can be reconstituted as circular dsDNA, if derived from plasmid or from viral DNA. We show that RecO, RecU, and Ku proteins, but not RecA, are important for plasmid transformation, and differentially accumulate at the polar DNA uptake machinery. Upon addition of any kind of DNA, the assembly of RecU at the competence pole dissipated, while RecA formed filamentous structures that rapidly grew and shrank within a 1 minute time scale. RecO visibly accumulated at the competence machinery only upon addition of plasmid DNA, but not of chromosomal DNA. In vitro, RecO was highly efficient at enhancing the annealing of complementary strands covered by SsbA, without the need for any nucleotide cofactor. The findings show that competent cells possess a dynamic recombination machinery and provide visual evidence for the existence of different pathways for transformation with chromosomal DNA or with plasmid DNA.

Objective analysis of the singing voice as a training aid

A new tool for robust tracking of fundamental frequency is proposed, along with an objective measure of main singing voice parameters, such as vibrato rate, vibrato extent, and vocal intonation. High-resolution Power Spectral Density estimation is implemented, based on AutoRegressive models of suitable order, allowing reliable formant tracking also in vocalizations characterized by highly varying values. The proposed techniques are applied to about 1000 vocalizations, coming from both professional and non-professional singers, and show better performance as compared to classical Fourier-based approaches. If properly implemented, and with a user-friendly interface, the new tool would allow real-time analysis of singing voice. Hence, it could be of help in giving non-professional singers and singing teachers reliable measures of possible improvements during and after training.