Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function

Substrate-binding proteins (SBPs) are used by organisms from the three domains of life for transport and signalling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here, we describe the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behaviour based on their connectivity, the discontinuous domain shows a stable native-like structure that binds l-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability and folding pathway of the lobes on their covalent association is most likely the result of the coevolution of both domains as a single unit.

De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2

We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo human angiotensin-converting enzyme 2 (hACE2) decoys to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The best monovalent decoy, CTC-445.2, bound with low nanomolar affinity and high specificity to the receptor-binding domain (RBD) of the spike protein. Cryo-electron microscopy (cryo-EM) showed that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, showed ~10-fold improvement in binding. CTC-445.2d potently neutralized SARS-CoV-2 infection of cells in vitro, and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.

De novo design of ACE2 protein decoys to neutralize SARS-CoV-2

There is an urgent need for the ability to rapidly develop effective countermeasures for emerging biological threats, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a generalized computational design strategy to rapidly engineer de novo proteins that precisely recapitulate the protein surface targeted by biological agents, like viruses, to gain entry into cells. The designed proteins act as decoys that block cellular entry and aim to be resilient to viral mutational escape. Using our novel platform, in less than ten weeks, we engineered, validated, and optimized de novo protein decoys of human angiotensin-converting enzyme 2 (hACE2), the membrane-associated protein that SARS-CoV-2 exploits to infect cells. Our optimized designs are hyperstable de novo proteins (∼18-37 kDa), have high affinity for the SARS-CoV-2 receptor binding domain (RBD) and can potently inhibit the virus infection and replication in vitro. Future refinements to our strategy can enable the rapid development of other therapeutic de novo protein decoys, not limited to neutralizing viruses, but to combat any agent that explicitly interacts with cell surface proteins to cause disease.

P966Clinical impact of target vessel on long term cardiac survival in patients with chronic total occlusion treated by percutaneous coronary intervention

Background

Chronic total occlusions (CTOs) occur in 15–35% of patients with significant coronary artery disease who undergo coronary angiography. The rationale of percutaneous CTO revascularization is the improvement in survival and in quality of life, mainly reducing angina symptoms and increasing LVEF. The clinical impact of target vessel has been investigated in previous studies, with controversial results.

Purpose

The aim of this study, based on a large scale single-center registry, is to determine the impact of different target vessel successful CTO percutaneous coronary intervention (PCI) on long-term survival in a “real world” population.

Methods

All consecutive patients who attempted a CTO-PCI from 2004 to 2015 in our Hospital department were included in a CTO-PCI Registry. CTO was defined as a coronary obstruction with TIMI flow grade 0 with an estimated duration of >3 months. Patients with multiple CTO were excluded. Long-term mortality was assessed by Kaplan-Meier and Cox multivariable analysis.

Results

A total of 1235 patients attempted PCI for CTO; patients were stratified into two main groups according to the CTO carrying vessel: LAD-CTO (n=360) and not-LAD CTO (n=875). Cardiac survival rate at 5 years was lower in LAD-CTO patients compared with not-LAD CTO patients (85±3% vs. 90±2%; p=0.001), but when a successful CTO-PCI was achieved, there was no statistical difference between the two groups (89±3% vs. 93±1%; p=0.095). On the other side, a failure of the CTO PCI in LAD vessel was associated with a worse outcome (67±8% vs. 85±4%; p=0.001). Completeness of revascularization carried a significant survival benefit independently from the target vessel CTO (LAD CTO group 94±2% vs. not-LAD CTO group 95±1%; p=0.256), but an incomplete revascularization was associated with a worse outcome in LAD-CTO patients (67±6% vs. 81±4%; p<0.001). By multivariable Cox analysis, age >75 years, diabetes, left ventricular ejection fraction <40%, complete revascularization and LAD-CTO were independently related to death.

Conclusions

In a “real world” population, LAD-CTOs were associated with a lower cardiac survival rate when compared to other vessel CTOs; however, this survival gap was no longer significant when a successful CTO PCI was performed. The survival benefit was even greater when a complete coronary revascularization was achieved.

Massively parallel de novo protein design for targeted therapeutics

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Expression analysis of phytochromes A, B and floral integrator genes during the entry and exit of grapevine-buds from endodormancy

A common molecular regulatory pathway that involves PHYA, PHYB and floral integrator genes CONSTANS (CO), FLOWERING LOCUS T (FT) and SUPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) has been suggested to participate in the regulation of photoperiod dependent processes such as flowering and dormancy. In grapevines (Vitis vinifera L.), decreasing photoperiod and low temperatures trigger the transition of buds into endodormancy (ED), a process that is accompanied by drastic changes in gene expression of VvPHYA and B in leaves. To analyse the relationship of VvPHYA, VvPHYB, and grape homologues of Arabidopsis floral integrator genes VvCO, VvFT, VvMADS8, with ED, a comparative expression analysis of these genes was performed in grapevine-leaves and buds before, during and after the transition of buds into ED. The expression of all the above genes in the bud-tissue, and the fact that photoperiod regulates differently the expression of VvPHYA and B in buds than in leaves, suggests that the bud might be an autonomous or semi-autonomous organ in perceiving and transducing the photoperiod signal. On the other hand, the coordinated down-regulation of VvFT in leaves and buds during the transition of buds into ED, and its subsequent up-regulation following the application of dormancy-breaking compounds, hydrogen cyanamide (HC) and sodium azide, suggests that VvFT could play a key role in stimulating bud-growth by repressing their entry into ED.

Elevated serum thyrotropin [TSH] levels in critically ill patients with acquired immunodeficiency syndrome (AIDS)

STUDY OBJECTIVE

To determine thyrotropin (TSH) reserve in critically ill patients with Acquired Immunodeficiency Syndrome (AIDS).

DESIGN

Prospective longitudinal.

SETTING

Six hundred (600) bed municipal hospital serving a poor neighborhood in New York City with a high incidence of AIDS mainly from intravenous drug abuse.

PATIENTS AND METHODS

Twelve (12) patients with AIDS, who were in the Intensive Care Unit or critically ill on medical wards, were evaluated consecutively with baseline thyroid function tests and serum thyrotropin (TSH) response to thyroid releasing hormone testing.

RESULTS

66.7% of patients had elevated TSH levels. All patients had low triiodothyronine (T3), six patients had low thyroxine (T4) levels.

RESULTS

(cont'd). Six patients met the criteria for hypothyroidism. Two patients met the criteria for subclinical hypothyroidism.

CONCLUSION

Elevated TSH levels and hypothyroidism are common in our critically ill population with AIDS.

HER-2/Neu overepression in gastric cancer

e15679

Background: Gastric cancer is one of the most frequent causes of cancer-related deaths in the world.Overexpression of human epidermal growth factor receptor 2 (HER-2) has been shown to be a significant negative prognostic variable, with estimates ranging from 6- 35%. This is the first study done in our country regarding HER-2 overexpresion in gastric cancer. Methods: 90 cases with histologic diagnosis of gastric cancer were reviewed, in the period between October 2007 and July 2008. Formalin-fixed paraffin- embedded gastric cancer specimens were tested for HER-2 status using Herceptest (Dako). They were analyzed with HER-2 scores for gastric cancer. Other parameters evaluated were: demographic, clinical, histological characteristics, and treatment administrared. Results: The average age of our patients was 60.3 ± 15.8 years, with similar gender distribution. The more frequent symptoms of presentation were loss of weight (68.9%) and dyspepsia (58.9%). The most frequent anatomical location was the antrum (32%). HER-2 overexpression was 5.6% (four cases of intestinal type and one case of diffuse type). 63.3% of the patients presented with clinical stage IV, which is associated with worse survival (p< 0.001). 40% of the patients underwent complete surgical excision of the neoplasia, from which 44% received adjuvant chemotherapy and radiotherapy. 52.2% of the patients had already died when developing this study. Conclusions: The majority of our patients presented with advange stage at the time of diagnosis, HER-2 overexpression was 5.6%. There was no statistical significance when comparing it with the histological type, nor survival (p= 0.086).

No significant financial relationships to disclose.

Consensus for tinnitus patient assessment and treatment outcome measurement: Tinnitus Research Initiative meeting, Regensburg, July 2006

There is widespread recognition that consistency between research centres in the ways that patients with tinnitus are assessed and outcomes following interventions are measured would facilitate more effective co-operation and more meaningful evaluations and comparisons of outcomes. At the first Tinnitus Research Initiative meeting held in Regensburg in July 2006 an attempt was made through workshops to gain a consensus both for patient assessments and for outcome measurements. It is hoped that this will contribute towards better cooperation between research centres in finding and evaluating treatments for tinnitus by allowing better comparability between studies.

Spontaneous voltage oscillations in striatal projection neurons in a rat corticostriatal slice

In a rat corticostriatal slice, brief, suprathreshold, repetitive cortical stimulation evoked long-lasting plateau potentials in neostriatal neurons. Plateau potentials were often followed by spontaneous voltage transitions between two preferred membrane potentials. While the induction of plateau potentials was disrupted by non-NMDA and NMDA glutamate receptor antagonists, the maintenance of spontaneous voltage transitions was only blocked by NMDA receptor and L-type Ca2+ channel antagonists. The frequency and duration of depolarized events, resembling up-states described in vivo, were increased by NMDA and L-type Ca2+ channel agonists as well as by GABAA receptor and K+ channel antagonists. NMDA created a region of negative slope conductance and a positive slope crossing indicative of membrane bistability in the current-voltage relationship. NMDA-induced bistability was partially blocked by L-type Ca2+ channel antagonists. Although evoked by synaptic stimulation, plateau potentials and voltage oscillations could not be evoked by somatic current injection--suggesting a dendritic origin. These data show that NMDA and L-type Ca2+ conductances of spiny neurons are capable of rendering them bistable. This may help to support prolonged depolarizations and voltage oscillations under certain conditions.

Relationship between occlusal curvatures and mandibular deviation in orthodontic patients with temporomandibular disorders

The aim of this study was to investigate the relationships between occlusal curvature (OC) and frontal craniofacial morphology in patients with and without temporomandibular disorders (TMD), using frontal cephalograms and a sophisticated measuring device (XYZAX S400A). Thirty-seven female orthodontic patients (mean age 24.0 years) were divided into a TMD group (n = 25) and no-TMD group (n = 12). In the TMD group, the lateral OCs of the mandibular second premolar, and first and second molars were significantly deeper on the deviated side than on the non-deviated side, and the anteroposterior OCs of the mandibular second premolar and first molar were also significantly shallower on the deviated side. In the no-TMD group, however, there were no significant differences in OCs between deviated and non-deviated sides. The differences between right and left lateral OCs in the mandibular second premolar and first and second molars, as well as the anteroposterior OCs in the mandibular first and second molars, showed significant correlations with mandibular deviation in the TMD group. On the other hand, in the no-TMD group, there was no significant correlation between OCs and mandibular deviation. The above results suggest that OCs might try to compensate for mandibular deviation in patients with TMD.

Reduction mammaplasty with superior-lateral dermoglandular pedicle: another alternative

During a period of 7.5 years, reduction mammaplasty using a superior-lateral dermoglandular pedicle was performed in 213 mammary glands in 112 patients. This procedure is a modification of the original technique by Skoog that takes advantage of its benefits but adds two basic premises: (1) to preserve the integrity of the galactophorous ducts for future nursing and (2) to cause less innervation injury. Patients were followed for an average of 28 months (range, 3 months to 7.5 years). The quantity of extirpated tissue ranged from 310 to 1380 g, with a median of 520 g. The nipple-areola complex migrated 5 to 14.5 cm (median, 7.8 cm). The most severe complication was partial necrosis of the nipple-areola complex, which occurred in five cases (four patients). This complication occurred only during the first 2 years of the study, in breast resections larger than 800 g, and with migrations larger than 10 cm. This problem resulted in a modification of the technique, and the complication has not occurred for the past 5 years. There were no important alterations in the sensibility of the nipple-areola complex nor in the integrity of the galactophorous ducts. The long-term satisfaction of the patients was high. The authors present an easily designed and accomplishable technique that is applicable to patients with severe hypertrophy and gigantomastia. The technique has a high security index, and the integrity of the mammary gland is maintained to the maximum.

Genetic variation in Fitzroya cupressoides (alerce), a threatened South American conifer

Fitzroya cupressoides (alerce, Cupressaceae) is a large and exceptionally long-lived conifer, endemic to a restricted area of southern Chile and neighbouring areas of Argentina. As a result of its high economic value, the species has been severely exploited for timber, and remnant populations are fragmented and often highly disturbed. The species is thought to have undergone a major range contraction during the last glaciation. In order to assess the extent of genetic variation using DNA markers within and between populations of this species, samples were obtained from throughout the natural range and analysed for random amplified polymorphic DNA (RAPD) variation. Eight 10-mer and three 15-mer primers were used to produce a total of 54 polymorphic bands. Shannon's diversity estimates were calculated to provide an estimate of the degree of variation within each population. Values varied from 0.343 to 0.636 with only the lowest value differing significantly from the others (Spop = 0.547). This indicated that there is a significant degree of variation within each population, and did not provide evidence for genetic 'bottle-neck' effects within the species. A pairwise distance measure calculated from the RAPD data was used as an input for principal coordinate (PCO) and AMOVA analyses. The first three principal coordinates of RAPD distances described 8.3, 5.9 and 5.4% of the total variance, respectively, and a degree of clustering of samples according to their geographical origin was detectable. AMOVA analysis indicated that although most of the variation (85.6%) was found within populations, a significant proportion (P < 0.002) was attributable to differences between populations. An UPGMA dendrogram constructed using phi ST values derived from AMOVA produced a pattern broadly similar to that produced by the PCO, highlighting differences between three main groups of populations within Chile: those from the northern Coastal Range, the southern Coastal Range and Central Depression, and the Andes. Populations from Argentina also emerged as significantly different from those in Chile. These results are interpreted in the context of the postglacial history of the species, and their implications for the development of conservation strategies for Fitzroya are discussed.

Intramuscular gluteal implants

The authors present a new space for the placement of gluteal implants in augmentation gluteoplasty. Placement of implants in this intramuscular anatomical space offers a good cosmetic result and seems to satisfy the demands of augmentation gluteoplasty in terms of safety, reproducibility, and esthetics.

Glucocorticoid reserve in patients with acquired immunodeficiency syndrome

The purpose of the study was to determine the glucocorticoid reserve in patients with AIDS. Thirty patients with AIDS, who were not critically ill, were chosen consecutively and studied prospectively over a 1-year period with cosyntropin-stimulation testing. All patients showed normal glucocorticoid response to cosyntropin stimulation. Clinical adrenal insufficiency is uncommon in patients with AIDS who are not critically ill.

Reversible variations in the methylation pattern of carrot DNA during somatic embryogenesis

Twenty five clones from a carrot genomic library were used as probes to detect variations in the 5-methyl-cytosine pattern during somatic embryogenesis. The majority of them evidenced an invariant pattern. With two clones however, differences were found between the adulttype DNA pattern and the embryonic one. The level of transcription of the relevant DNA fragments during embryogenesis was investigated by Northern blotting. One of the two probes did not show signals in any of the developmental stages whereas the other showed developmentally regulated expression. This fact suggests a novel strategy for cloning developmentally expressed functions.

DNA methylation of embryogenic carrot cell cultures and its variations as caused by mutation, differentiation, hormones and hypomethylating drugs

The level of auxin - both natural and synthetic - in the medium has a strong effect on the level of 5-methyl-cytosine in the DNA of carrot cells in culture. This level may vary from approximately 15% to 70% of total cytosine without apparent effects on growth rate and cell morphology. No effect was seen with cytokinin. During somatic embryogenesis, in the absence of hormones, variations were seen in the level of methylation according to a characteristic pattern. If hypomethylation is induced with drugs such as azacytidine, ethionine or ethoxy-carbonyl-pyrimidine, embryogenesis is immediately blocked. A mutant was isolated which is resistant to the action of hypomethylating drugs. It shows variations in the methylation pattern and variations in indole-acetic acid metabolism. In addition its regeneration is often associated with the production of tumors.

Studies of mutagenicity on quiescent and proliferating hamster cell populations

A few known mutagens were tested on proliferating hamster cells and on cells made quiescent by L-histidinol block. No differences were found in the effectiveness of two alkylating agents and a base analogue; whereas the carcinogen 4-nitroquinoline-1-oxide was more effective on quiescent than on proliferating cells. The implications of these data on the mechanism of action of mutagens are discussed.