A family of thermostable fungal cellulases created by structure-guided recombination

SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of 48 genes sampled from the 6,561 possible chimeric sequences were secreted by the Saccharomyces cerevisiae heterologous host in catalytically active form. Five of these chimeras have half-lives of thermal inactivation at 63°C that are greater than the most stable parent, CBH II enzyme from the thermophilic fungus Humicola insolens, which suggests that this chimera collection contains hundreds of highly stable cellulases. Twenty-five new sequences were designed based on mathematical modeling of the thermostabilities for the first set of chimeras. Ten of these sequences were expressed in active form; all 10 retained more activity than H. insolens CBH II after incubation at 63°C. The total of 15 validated thermostable CBH II enzymes have high sequence diversity, differing from their closest natural homologs at up to 63 amino acid positions. Selected purified thermostable chimeras hydrolyzed phosphoric acid swollen cellulose at temperatures 7 to 15°C higher than the parent enzymes. These chimeras also hydrolyzed as much or more cellulose than the parent CBH II enzymes in long-time cellulose hydrolysis assays and had pH/activity profiles as broad, or broader than, the parent enzymes. Generating this group of diverse, thermostable fungal CBH II chimeras is the first step in building an inventory of stable cellulases from which optimized enzyme mixtures for biomass conversion can be formulated

Chiral Effective Lagrangian and Quark Masses

The status of lattice determinations of quark masses is reviewed (with the exception of m_b). Attempts to extract the low-energy constants in the effective chiral Lagrangian are discussed, with special emphasis on those couplings which are required to test the hypothesis of a massless up-quark. Furthermore, the issue of quenched chiral logarithms is addressed.Comment: Invited talk presented at Lattice2002(plenary), 12 pages, 3 figure

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.Comment: to appear in Biophysical Journal (2009). to appear in Biophysical Journal (2009

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

A simple proof of Kotake-Narasimhan theorem in some classes of ultradifferentiable functions

[EN] We give a simple proof of a general theorem of Kotake-Narasimhan for elliptic operators in the setting of ultradifferentiable functions in the sense of Braun, Meise and Taylor. We follow the ideas of Komatsu. Based on an example of Metivier, we also show that the ellipticity is a necessary condition for the theorem to be true.C. Boiti and D. Jornet were partially supported by the INdAM-GNAMPA Projects 2014 and 2015. D. Jornet was partially supported by MINECO, Project MTM2013-43540-PBoiti, C.; Jornet Casanova, D. (2017). A simple proof of Kotake-Narasimhan theorem in some classes of ultradifferentiable functions. Journal of Pseudo-Differential Operators and Applications. 8(2):297-317. https://doi.org/10.1007/s11868-016-0163-yS29731782Boiti, C., Jornet, D.: The problem of iterates in some classes of ultradifferentiable functions. Oper. Theory Adv. Appl. Birkhauser Basel 245, 21–33 (2015)Boiti, C., Jornet, D.: A characterization of the wave front set defined by the iterates of an operator with constant coefficients. arXiv:1412.4954Boiti, C., Jornet, D., Juan-Huguet, J.: Wave front set with respect to the iterates of an operator with constant coefficients. Abstr. Appl. Anal. 2014, 1–17 Article ID 438716 (2014). doi: 10.1155/2014/438716Bolley, P., Camus, J., Mattera, C.: Analyticité microlocale et itérés d’operateurs hypoelliptiques. Séminaire Goulaouic-Schwartz, 1978–1979, Exp No. 13, École Polytech, PalaiseauBonet, J., Meise, R., Melikhov, S.N.: A comparison of two different ways of define classes of ultradifferentiable functions. Bull. Belg. Math. Soc. Simon Stevin 14, 425–444 (2007)Braun, R.W., Meise, R., Taylor, B.A.: Ultradifferentiable functions and Fourier analysis. Result. Math. 17, 206–237 (1990)Fernández, C., Galbis, A.: Superposition in classes of ultradifferentiable functions. Publ. Res. I Math. Sci. 42(2), 399–419 (2006)Jornet Casanova, D.: Operadores Pseudodiferenciales en Clases no Casianalíticas de Tipo Beurling. Universitat Politècnica de València (2004). doi: 10.4995/Thesis/10251/54953Juan-Huguet, J.: Iterates and hypoellipticity of partial differential operators on non-quasianalytic classes. Integr. Equ. Oper. Theory 68, 263–286 (2010)Juan-Huguet, J.: A Paley–Wiener type theorem for generalized non-quasianalytic classes. Stud. Math. 208(1), 31–46 (2012)Komatsu, H.: A characterization of real analytic functions. Proc. Jpn Acad. 36, 90–93 (1960)Komatsu, H.: On interior regularities of the solutions of principally elliptic systems of linear partial differential equations. J. Fac. Sci. Univ. Tokyo Sect. 1, 9, 141–164 (1961)Komatsu, H.: A proof of Kotaké and Narasimhan’s theorem. Proc. Jpn Acad. 38(9), 615–618 (1962)Kotake, T., Narasimhan, M.S.: Regularity theorems for fractional powers of a linear elliptic operator. Bull. Soc. Math. Fr. 90, 449–471 (1962)Kumano-Go, H.: Pseudo-Differential Operators. The MIT Press, Cambridge, London (1982)Langenbruch, M.: P-Funktionale und Randwerte zu hypoelliptischen Differentialoperatoren. Math. Ann. 239(1), 55–74 (1979)Langenbruch, M.: Fortsetzung von Randwerten zu hypoelliptischen Differentialoperatoren und partielle Differentialgleichungen. J. Reine Angew. Math. 311/312, 57–79 (1979)Langenbruch, M.: On the functional dimension of solution spaces of hypoelliptic partial differential operators. Math. Ann. 272, 217–229 (1985)Langenbruch, M.: Bases in solution sheaves of systems of partial differential equations. J. Reine Angew. Math. 373, 1–36 (1987)Lions, J.L., Magenes, E.: Problèmes aux limites non homogènes et applications, vol. 3. Dunod, Paris (1970)Métivier, G.: Propriété des itérés et ellipticité. Commun. Part. Differ. Eq. 3(9), 827–876 (1978)Nelson, E.: Analytic vectors. Ann. Math. 70, 572–615 (1959)Newberger, E., Zielezny, Z.: The growth of hypoelliptic polynomials and Gevrey classes. Proc. Am. Math. Soc. 39(3), 547–552 (1973)Oldrich, J.: Sulla regolarità delle soluzioni delle equazioni lineari ellittiche nelle classi di Beurling. (Italian) Boll. Un. Mat. Ital. (4) 2, 183–195 (1969)Petzsche, H.-J., Vogt, D.: Almost analytic extension of ultradifferentiable functions and the boundary values of holomorphic functions. Math. Ann. 267(1), 17–35 (1984

Nucleation phenomena in protein folding: The modulating role of protein sequence

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear

A time-frequency analysis perspective on Feynman path integrals

The purpose of this expository paper is to highlight the starring role of time-frequency analysis techniques in some recent contributions concerning the mathematical theory of Feynman path integrals. We hope to draw the interest of mathematicians working in time-frequency analysis on this topic, as well as to illustrate the benefits of this fruitful interplay for people working on path integrals.Comment: 26 page

Preliminary checklist of orchids in the Sungai Kangkawat, Imbak Canyon Conservation Area (ICCA), Sabah, Malaysia

A study on orchids diversity was carried out in the Sungai Kangkawat, Imbak Canyon Conservation Area (ICCA), Sabah, Malaysia. The study aimed to record species composition and distribution of orchids in the furtherance of orchid conservation objective in the gazetted conservation area. A total of 95 species and 30 genera were collected from South Rim, Kawang, and Nepenthes trails. The collection consists of 91 epiphytes, two terrestrials, and two mycoheterotrophs. More orchids were found in the riverine than inland areas. Our study on the species composition based on the vegetation types shows that the presence of inconspicuous and achlorophyllous, either mycoheterotrophic or leafless epiphytic orchids, are indicators of the undisturbed vegetation types. Though the finding was preliminary and brief, our encounter of endemic and rare species underlines the importance of Sungai Kangkawat forest area as an orchid biodiversity hotspot

The incidence, aetiology and outcome of acute seizures in children admitted to a rural Kenyan district hospital

<p>Abstract</p> <p>Background</p> <p>Acute seizures are a common cause of paediatric admissions to hospitals in resource poor countries and a risk factor for neurological and cognitive impairment and epilepsy. We determined the incidence, aetiological factors and the immediate outcome of seizures in a rural malaria endemic area in coastal Kenya.</p> <p>Methods</p> <p>We recruited all children with and without seizures, aged 0–13 years and admitted to Kilifi District hospital over 2 years from 1^stDecember 2004 to 30^thNovember 2006. Only incident admissions from a defined area were included. Patients with epilepsy were excluded. The population denominator, the number of children in the community on 30^thNovember 2005 (study midpoint), was modelled from a census data.</p> <p>Results</p> <p>Seizures were reported in 900/4,921(18.3%) incident admissions and at least 98 had status epilepticus. The incidence of acute seizures in children 0–13 years was 425 (95%CI 386, 466) per 100,000/year and was 879 (95%CI 795, 968) per 100,000/year in children <5 years. This incidence data may however be an underestimate of the true incidence in the community. Over 80% of the seizures were associated with infections. Neonatal infections (28/43 [65.1%]) and falciparum malaria (476/821 [58.0%]) were the main diseases associated with seizures in neonates and in children six months or older respectively. Falciparum malaria was also the main illness (56/98 [57.1%]) associated with status epilepticus. Other illnesses associated with seizures included pyogenic meningitis, respiratory tract infections and gastroenteritis. Twenty-eight children (3.1%) with seizures died and 11 surviving children (1.3%) had gross neurological deficits on discharge. Status epilepticus, focal seizures, coma, metabolic acidosis, bacteraemia, and pyogenic meningitis were independently associated with mortality; while status epilepticus, hypoxic ischaemic encephalopathy and pyogenic meningitis were independently associated with neurological deficits on discharge.</p> <p>Conclusion</p> <p>There is a high incidence of acute seizures in children living in this malaria endemic area of Kenya. The most important causes are diseases that are preventable with available public health programs.</p

Atrial fibrillation and heart failure: Factors influencing the choice of oral anticoagulant.

Atrial fibrillation (AF) and heart failure (HF) frequently coexist. AF is identified in approximately one third of patients with HF and is linked to increased morbidity and mortality than from either condition alone. AF is relatively more common in HF with preserved ejection fraction (HFpEF) than with reduced ejection fraction (HFrEF). Nevertheless, the risk of stroke and systemic embolism (SSE) is significantly increased with both HF types and the absolute risk is heavily influenced by the presence and severity of associated additional stroke risk factors. The European Society of Cardiology has very recently introduced a third HF subtype entitled HF with mid-range ejection fraction (HFmrEF). At present oral anticoagulation is recommended for all patients with AF and HF, independent of HF type. In addition to warfarin there are currently four non-vitamin K oral anticoagulants (NOACs, previously called novel oral anticoagulants) that have been approved for the prevention of SSE. They consist of one direct thrombin inhibitor, dabigatran and three factor Xa inhibitors: rivaroxaban, apixaban and, most recently, edoxaban. In this review article we present an overview of the evidence to support the use of NOACs for the prevention of SSE in patients with AF and HF and review the influence of HF subtype and co-morbidities on the potential choice of oral anticoagulant