CHALLENGES IN MATCHING SECONDARY STRUCTURES IN CRYO-EM: AN EXPLORATION

Cryo-electron microscopy is a fast emerging biophysical technique for structural determination of large protein complexes. While more atomic structures are being determined using this technique, it is still challenging to derive atomic structures from density maps produced at medium resolution when no suitable templates are available. A critical step in structure determination is how a protein chain threads through the 3-dimensional density map. A dynamic programming method was previously developed to generate K best matches of secondary structures between the density map and its protein sequence using shortest paths in a related weighted graph. We discuss challenges associated with the creation of the weighted graph and explore heuristic methods to solve the problem of matching secondary structures.

A novel missense mutation in the FGB gene (p.Gly302Arg) leading to afibrinogenemia. Predicted structure and function consequences

Afibrinogenemia represents the rarest form of fibrinogen deficiency. Causative missense mutations occur rarely and may improve the understanding of fibrinogen structure and function.

PATIENTS AND METHODS

The propositus was a 26-year-old Argentinian with afibrinogenemia. FGA, FGB and FGG exons and flanking regions were screened by sequencing and the mutant protein was analyzed in silico.

RESULTS

A novel missense mutation in the FGB gene (Bbeta Gly272Arg, p.Gly302Arg) was identified. In silico analysis revealed its location in a highly conserved region, which preserves the core fold of the C-terminal beta-chain and is important for proper secretion. A substitution by a positively charged large Arg residue in this area would most likely disturb the core fold by additional interactions with adjacent residues (p.Asp291, p.Asp297, p.Asp311), or by forming of non-native interactions with other proteins, thereby hindering the action of molecular chaperones. Both alternatives would disturb the regular secretion of the beta-chain.

CONCLUSIONS

The novel missense mutation in the FGB gene causes afibrinogenemia most probably by affecting the secretion of the fibrinogen beta-chain.

Combined coagulation factor VIII and factor IX deficiency (CDF8F9) in a patient from Lithuania

Haemophilia A (FVIII deficiency) and haemophilia B (FIX deficiency) are X-linked inherited bleeding disorders. It is a very rare event to identify both haemophilias in the same patient. So far, only two families with such combination are reported in the literature worldwide supported by genetic background.

PATIENTS AND METHODS

Evaluation of clinical data, determination of FVIII and FIX levels and genetic analysis of F8 and F9 genes by direct sequencing.

RESULTS

We report on a patient having severe haemophilia B (FIX:C <1 IU dl^-1) and mild haemophilia A (FVIII:C 18 IU dl^-1 ). FIX deficiency was known since childhood, whereas mild haemophilia A was confirmed at the age of 42 due to unexpected bleeding complications after dental extraction despite adequate substitution with plasma derived FIX concentrate. F9 gene analysis showed a point mutation in exon 2 (c.223C>T, p.R75X), whereas F8 gene analysis revealed a point mutation in exon 4 (c.545A>C, p.D182A). The mother of the patient was heterozygous for F8 mutation, but not for F9 mutation suggesting a de novo F9 mutation. Accidentally, further family from Germany with mild Haemophilia A was identified to have the same F8 mutation. F8 Haplotype analysis revealed that the p.D182A mutation most likely represents a founder mutation with common ancestors of the German and the Lithuanian family.

CONCLUSIONS

Our results confirm the rare event of Haemophilia A and haemophilia B in the same patient originating from two distinct genetic defects in F8 and F9 genes.

Chemoradiotherapy for squamous cell anal carcinoma: a review of prognostic factors

AIM

Previous literature has sought prognostic factors for the survival of anal cancer patients. The present study aimed to determine prognostic factors for local disease recurrence, distant metastasis and survival for patients treated with radical chemoradiotherapy (CRT) at the Rosemere Cancer Centre, Preston, UK.

METHOD

Patients treated with CRT for nonmetastatic squamous cell anal cancer between September 2000 and January 2013 were studied. Kaplan-Meier and Cox regression analysis assessed the prognostic value of age, sex, tumour size, the proportion of the anal canal circumference involved (ACCI), nodal disease, tumour location and pretreatment haemoglobin.

RESULTS

One hundred and 48 patients with a mean age of 63 years were studied, of whom 15% suffered local disease recurrence and 10% developed distant metastasis. The 5-year overall and cancer-specific survival rates were 84% and 86%, respectively. Predictors of local recurrence were tumour size >5 cm and over two-thirds ACCI (P < 0.01). Predictors of distant metastasis and poor survival were tumour size >5 cm (P < 0.01), node positive disease on imaging (P < 0.05), over two-thirds ACCI (P < 0.01) and a pretreatment haemoglobin level below 130 g/l (P < 0.05). Multivariate analysis found large tumour size to be the most significant factor for local recurrence (P = 0.002) and survival (P = 0.02) whilst over two-thirds ACCI was most predictive of distant metastasis (P < 0.001). Age, gender, palpable lymph nodes and tumour location were not of prognostic value for local disease recurrence, distant metastasis or survival.

CONCLUSION

Tumour size, nodal disease, over two-thirds ACCI and low pretreatment haemoglobin confer poorer prognostic and survival outcomes. Use of intensity-modulated radiation therapy may allow greater radiation doses to be given for locally advanced tumours, thus improving local control and survival and reducing morbidity.

Custom-made silicone hand prosthesis: A case study

Up to now, a cosmetic glove was the most common method for managing transmetacarpal (TMC) and carpometacarpal (CMC) amputations, but it is devoid of markings and body color. At this amputation level, it is very difficult to fit a functional prosthesis because of the short available length, unsightly shape, grafted skin, contracture and lack of functional prosthetic options. A 30-year-old male came to our clinic with amputation at the 1st to 4th carpometacarpal level and a 5th metacarpal that was projected laterally and fused with the carpal bone. The stump had grafted skin, redness, and an unhealed suture line. He complained of pain projected over the metacarpal and suture area. The clinical team members decided to fabricate a custom-made silicone hand prosthesis to accommodate the stump, protect the grafted skin, improve the hand's appearance and provide some passive function. The custom silicone hand prosthesis was fabricated with modified flexible wires to provide passive interphalangeal movement. Basic training, care and maintenance instructions for the prosthesis were given to the patient. The silicone hand prosthesis was able to restore the appearance of the lost digits and provide some passive function. His pain (VAS score) was reduced. Improvement in activities of daily living was found in the DASH questionnaire and Jebsen-Taylor Hand Function test. A silicone glove is a good option for more distal amputations, as it can accommodate any deformity, protect the skin, enhance the appearance and provide functional assistance. This case study provides a simple method to get passively movable fingers after proximal hand amputation.

Accuracy of ultrasound dating formulae in the late second-trimester in pregnancies conceived with in-vitro fertilization

Purpose: To investigate the accuracy of ultrasound dating formulae in the late second trimester of pregnancy.

Material and Methods: A dataset of 136 singleton pregnancies conceived by artificial reproductive techniques was studied to assess the accuracy of ultrasound dating formulae in the late second trimester, and compared with early second trimester. A total of 21 published ultrasound-dating formulae were tested.

Results: For most formulae, late second trimester scans yielded results that were marginally less accurate than the early second trimester. The best performance was obtained with dating formulae based on femur length, either alone or combined with the biparietal diameter. These formulae had mean absolute errors of 3–3.5 days. Combining two or more parameters did not result in any substantial gain in accuracy.

Conclusions: Pregnancy dating by ultrasound in the late second trimester is sufficiently accurate for routine clinical use. Formulae based on femur length appear to be at least as accurate as head measurements.

Composition dependence of charge and magnetic length scales in mixed valence manganite thin films

Mixed-valence manganese oxides present striking properties like the colossal magnetoresistance, metal-insulator transition (MIT) that may result from coexistence of ferromagnetic, metallic and insulating phases. Percolation of such phase coexistence in the vicinity of MIT leads to first-order transition in these manganites. However the length scales over which the electronic and magnetic phases are separated across MIT which appears compelling for bulk systems has been elusive in (La_1−yPr_y)_1−xCa_xMnO₃ films. Here we show the in-plane length scale over which charge and magnetism are correlated in (La_0.4Pr_0.6)_1−xCa_xMnO₃ films with x = 0.33 and 0.375, across the MIT temperature. We combine electrical transport (resistance) measurements, x-ray absorption spectroscopy (XAS), x-ray magnetic circular dichroism (XMCD), and specular/off-specular x-ray resonant magnetic scattering (XRMS) measurements as a function of temperature to elucidate relationships between electronic, magnetic and morphological structure of the thin films. Using off-specular XRMS we obtained the charge-charge and charge-magnetic correlation length of these LPCMO films across the MIT. We observed different charge-magnetic correlation length for two films which increases below the MIT. The different correlation length shown by two films may be responsible for different macroscopic (transport and magnetic) properties.

Identification and functional characterization of a novel F5 mutation (Ala512Val, FVB onn ) associated with activated protein C resistance

Essentials Activated protein C (APC) resistance is a prevalent risk factor for venous thrombosis. A novel missense mutation (Ala512Val - FVBonn ) was characterized in vitro and in silico. FVBonn is a new cause of APC resistance and venous thrombosis. FVBonn expresses additionally enhanced procoagulant activity in the absence of APC.

SUMMARY

Background Activated protein C (APC) resistance is a prevalent risk factor for venous thrombosis. This phenotype is most commonly associated with the factor V Arg506Gln mutation (FV Leiden), which impairs the APC-mediated inactivation of both activated FV (FVa) and activated FVIII (FVIIIa). Objectives Here, we report the identification and characterization of a novel FV mutation (Ala512Val, FVBonn ) in six patients with APC resistance and venous thrombosis or recurrent abortions. Methods FVBonn was expressed in a recombinant system and compared with recombinant wild-type (WT) FV and FV Leiden in several functional assays. Results FVBonn conferred APC resistance to FV-depleted plasma, both in the activated partial thromboplastin time (APTT)-based test (APC sensitivity ratio [APCsr] of 1.98 for FVBonn versus 4.31 for WT FV and 1.59 for FV Leiden) and in the thrombin generation-based test (normalized APCsr of 5.41 for FVBonn versus 1.00 for WT FV and 8.99 for FV Leiden). The APC-mediated inactivation of FVaBonn was slower than that of WT FVa (mainly because of delayed cleavage at Arg506), but was greatly stimulated by protein S. The APC cofactor activity of FVBonn in FVIIIa inactivation was ~ 24% lower than that of WT FV. In line with these findings, an in silico analysis showed that the Ala512Val mutation is located in the same loop as the Arg506 APC cleavage site and might hamper its interaction with APC. Moreover, FVBonn was more procoagulant than WT FV and FV Leiden in the absence of APC, because of an increased activation rate and, possibly, an enhanced interaction with activated FX. Conclusions FVBonn induces hypercoagulability via a combination of increased activation/procoagulant activity, decreased susceptibility to APC-mediated inactivation, and slightly reduced APC cofactor activity.

Clinico-Hematologic Profile of Factor XIII-Deficient Patients

A retrospective analysis of clinico-hematologic parameters of 18 factor XIII-deficient patients was carried out. The hematologic tests included activated partial thromboplastin time (APTT), prothrombin time (PT), and clot solubility. Laboratory diagnosis of FXIII deficiency was made where bleeding time, PT, APTT, and thrombin time were normal and the clot solubility test result with 5M urea was positive. Factor XIII level with family screening was performed using commercially available kits. History of prolonged bleeding from the umbilical stump was present in four (22.2%) patients. The most common site of bleeding was the skin (11 of 18 patients). Three patients were given prophylaxis (FFP in two, factor XIII in one). A high prevalence of recurrent abortion in female pa tients with FXIII deficiency (two of the three patients in this study) was observed.

Clinicohematologic Spectrum in Patientswith Lupus Anticoagulant

A retrospective analysis of clinicohematologic parameters of 25 patients with lupus anticoagulant was carried out. The hematologic tests included dilute Russel viper venom test (dRVVT), kaolin clotting time (KCT), activated partial thromboplastin time, and prothrombin time. The diagnosis of lupus anticoagulants was based on the presence of prolonged KCT/dRVVT, its absence of correction with normal plasma and correction by phospholipids. Specific factor assays and platelet aggregation studies were performed wherever required. Ten patients (40%) had thrombosis, which was venous in 5 (50%) and arterial in 4 (40%). One patient (10%) had both arterial and venous thrombosis and presented with catastrophic antiphospholipid syndrome. Eighteen female patients conceived. Four (22%) of these had recurrent first trimester abortion. Five (20%) patients had bleeding manifestations. One (4%) of these had hypoprothrombinemia and was diagnosed to have hypoprothrombinemia lupus anticoagulant syndrome. However in two of these patients, no cause of bleeding could be identified other than the presence of lupus anticoagulants. It is concluded that patients with lupus anticoagulant have a varied spectrum of hemostatic disorders. Bleeding may sometimes occur in these patients due to associated thrombocytopenia or associated factor inhibitors. Rarely, it may occur due to presence of lupus anticoagulants alone.

Management of chronic empyema with unexpandable lung in poor surgical risk patients using an empyema tube

Objectives:

High preoperative risk precludes decortication and other surgical interventions in some patients with chronic empyema. We manage such patients by converting the chest tube into an “empyema tube,” cutting the tube near the skin and securing the end with a sterile clip to allow for open pleural drainage. The patient is followed serially, and the tube gradually withdrawn based on radiological resolution and amount of drainage.

Methods:

Between 2010 and 2014, patients with chronic empyema and unexpandable lung, deemed high-risk surgical candidates, had staged chest tube removal, and were included for the study. The volume of fluid drained, culture results, duration of drainage, functional status, and comorbidities were recorded.

Measurements and Results:

Eight patients qualified. All had resolution of infection. The tube was removed after an average of 73.6 ± 49.73 (95% confidence interval [CI]) days. The mean duration of antibiotic treatment was 5.37 ± 1.04 (95% CI) weeks. None required surgery or experienced complications from an empyema tube.

Conclusion:

A strategy of empyema tube drainage with staged removal is an option in appropriately selected patients with chronic empyema, unexpandable lung, and poor surgical candidacy.

Tricky typhus ticks two: A report of two sisters from North India presenting with acute respiratory distress syndrome due to scrub typhus

Scrub typhus is emerging as an important cause of acute febrile illness in Northern India. This is a report of two sisters presenting concurrently with acute respiratory distress syndrome. A diagnosis of scrub typhus was made in both the patients, and they were successfully treated with doxycycline.

Management of Intrapleural Sepsis with Once Daily Use of Tissue Plasminogen Activator and Deoxyribonuclease

BACKGROUND

Pleural infection remains a significant cause of morbidity, mortality, prolonged hospital stay, and increased healthcare costs, despite advances in therapy. Twice daily intrapleural tissue plasminogen activator (tPA)/deoxyribonuclease (DNase) initiated at the time of diagnosis has been shown to significantly improve radiological outcomes and decrease the need for surgery.

OBJECTIVES

To analyze our experience with once daily tPA/DNase for intrapleural sepsis.

METHODS

Data derived from consecutive patients with empyema and complicated parapneumonic effusion who received once daily intrapleural tPA/DNase between January 2012 and August 2014 were reviewed. Measured outcomes included treatment success at 30 days, volume of pleural fluid drained, improvement in radiographic pleural opacity, length of hospital stay, need for surgery, and adverse events.

RESULTS

55 consecutive patients (33 male; mean age ± SD, 54.6 ± 16.1 years) were treated with once daily intrapleural tPA/DNase for 3 days. The majority of the patients (n = 51; 92.7%) were successfully managed without the need for surgical intervention. The mean change in pleural opacity measured on chest radiograph at day 7 was -28.8 ±17.6%. The median amount of fluid drained was 2,195 ml. No serious adverse events requiring discontinuation of intrapleural medications were observed. The most common complication was pain requiring escalating doses of analgesics (n = 8; 15%). Compliance with the protocol was excellent.

CONCLUSION

Early administration of once daily intrapleural tPA/DNase for 3 days is safe, effective, and represents a viable option for the management of empyema and complicated parapneumonic effusion.

Patient With Slow-Growing Mediastinal Mass Presents With Chest Pain and Dyspnea

A 52-year-old white woman presented with severe pain over the right upper abdomen and nonpleuritic, right-sided, lower chest-wall pain. Her pain had progressively gotten more frequent and severe over the last 5 months. It was also associated with a nonexertional, pressure-like sensation in the central chest. The patient denied any shortness of breath, fevers, cough, or any sputum production. She was taking levothyroxine for hypothyroidism and was a 30-pack-year current smoker; there was no history of drug abuse or occupational exposure. Previous chest radiographs dating back to 5 years consistently showed an elevated right-sided hemidiaphragm without any infiltrates or effusions; cardiomediastinal structures were unremarkable. She had not had a previous workup for these abnormal findings.

A novel missense mutation in the FGB gene (p.Gly302Arg) leading to afibrinogenemia

Afibrinogenemia represents the rarest form of fibrinogen deficiency. Causative missense mutations occur rarely and may improve the understanding of fibrinogen structure and function. Patients and methods: The propositus was a 26-year-old Argentinian with afibrinogenemia. FGA, FGB and FGG exons and flanking regions were screened by sequencing and the mutant protein was analyzed in silico. Results: A novel missense mutation in the FGB gene (Bbeta Gly272Arg, p.Gly302Arg) was identified. In silico analysis revealed its location in a highly conserved region, which preserves the core fold of the C-terminal beta-chain and is important for proper secretion. A substitution by a positively charged large Arg residue in this area would most likely disturb the core fold by additional interactions with adjacent residues (p.Asp291, p.Asp297, p.Asp311), or by forming of non-native interactions with other proteins, thereby hindering the action of molecular chaperones. Both alternatives would disturb the regular secretion of the beta-chain. Conclusions: The novel mis-sense mutation in the FGB gene causes afibrinogenemia most probably by affecting the secretion of the fibrinogen beta-chain.

Right heart failure in acute respiratory distress syndrome: An unappreciated albeit a potential target for intervention in the management of the disease

Mortality from acute respiratory distress syndrome (ARDS) has gone down recently. In spite of this trend, the absolute numbers continue to be high even with improvements in ventilator strategies and a better understanding of fluid management with this disease. A possible reason for this could be an under-recognized involvement of the pulmonary vasculature and the right side of the heart in ARDS. The right heart is not designed to function under situations leading to acute elevations in afterload as seen in ARDS, and hence it decompensates. This brief review focuses on the magnitude of the problem, its detection in the intensive care unit, and recognizes the beneficial effect of prone-positioning on the pulmonary vasculature and right heart.