Structure-based protein design with deep learning

Since the first revelation of proteins functioning as macromolecular machines through their three dimensional structures, researchers have been intrigued by the marvelous ways the biochemical processes are carried out by proteins. The aspiration to understand protein structures has fueled extensive efforts across different scientific disciplines. In recent years, it has been demonstrated that proteins with new functionality or shapes can be designed via structure-based modeling methods, and the design strategies have combined all available information — but largely piece-by-piece — from sequence derived statistics to the detailed atomic-level modeling of chemical interactions. Despite the significant progress, incorporating data-derived approaches through the use of deep learning methods can be a game changer. In this review, we summarize current progress, compare the arc of developing the deep learning approaches with the conventional methods, and describe the motivation and concepts behind current strategies that may lead to potential future opportunities.     

Microbial carbonate production in a starved basin: The crenistria Limestone of the upper Viséan German Kulm facies

The crenistria Limestone is a set of three autochthonous massive limestone beds occurring with great lithological persistence in the Kulm Facies (cd III , upper Viséan) of the eastern Rheinisches Schiefergebirge. Microfacies analysis reveals mainly minipeloidal fabrics and homogeneous micrite. Uncrushed, sediment-filled conchs of goniatites represent loci of sheltered preservation of primary carbonate textures. Calcified radiolarians are abundant, forming between 20 and 80% of total rock volume. The alleged algal genus Rectangulina is common in the crenistria Limestone. It is reinterpreted to represent the faeces of goniatites. For the first time the presence of in situ preserved sponges is reported. They can be recognized as delicate networks of microsparitic needles embedded in peloidal fabrics. Hexactinellids with primary spicule arrangements can be found embedded in homogeneous micrite. The carbonate forming the limestone beds was produced microbially during decomposition of soft tissue of the radiolarians and sponges. During the cd III , anoxia in the bottom waters of the Kulm Basin persisted for long periods due to stable density stratification of the water column under humid climatic conditions. Oxic conditions in the bottom waters during formation of the limestone are indicated by bioturbation, the presence of sponges and the high Mn-contents of the carbonate. The latter derived from reduction of Mn-oxides during microbial carbonate formation.     

Oxidatively Modified Plasma Phospholipids Containing Reactive Carbonyl Functions Measured by HPLC: Evidence for Phosphatidylcholine-Bound Aldehydes in Plasma of Burn Patients

A HPLC method has been developed to measure phosphatidylcholine (PC) containing reactive carbonyl functions in the sn-acyl residue in order to study processes in which such reactive carbonyls can be formed due to e.g. oxidative fragmentation. The method has been applied to determine PC-bound carbonyls as 2, 4-dinitrophenylhydrazones (DNPH) in plasma of burn patients. Plasma from healthy volunteers served as controls. Additionally, in vitro oxidation experiments (A: plasma, buffer diluted; B: plasma + iron-EDTA complex and C: plasma + iron-EDTA complex + H₂O₂) have been performed to obtain and to identify 2, 4-dinitrophenylhydrazine derivatizable carbonyl functions in plasma PC. Both, the PC-aldehydes and PC-aldehyde DNPH derivatives were cleavable with phospholipase C. Quantification was based on thin-layer chromatography purified soybean phosphatidylcholine, which was identically oxidized and derivatized as the plasma lipids in vitro.     

枯草杆菌BS224菌在防治Ⅲ°烧伤创面感染中痂下组织细菌数量的动态观察

对48例Ⅲ°烧伤病人的创面,定量植入枯草杆菌BS224菌后,分别在24h、48h、72h及96h做痂下组织细菌定量检测。结果显示:枯草杆菌对痂下组织的致病菌有明显的拮抗作用。感染创面的BS224菌体数量24—48小时显著增加,72—96小时而下降。与清洁创面的BS224菌动态变化上相同,呈常态曲线的规律变化。     

Ameliorative effects of clindamycin - nanoceria conjugate: A ROS responsive smart drug delivery system for diabetic wound healing study

BackgroundIncreased incidence of antibiotic-resistant species calls for development of new types of nano-medicine that can be used for healing of bacteria-caused wounds, such as diabetic foot ulcer. As diabetic patients have inefficient defense mechanism against reactive oxygen species (ROS) produced in our body as a by-product of oxygen reduction, the process of wound healing takes longer epithelialisation period. Ceria nanoparticles (CNPs) are well-known for their antibacterial and ROS-scavenging nature. Yet till now no significant effort has been made to conjugate ceria nanoparticles with drugs to treat diabetic wounds.MethodsIn this experiment, CNPs were synthesized in-house and clindamycin hydrochloride was loaded onto it by physical adsorption method for reactive oxygen species responsive drug delivery. Various physico-chemical characterisations such as Transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, Energy dispersive X-ray, Thermogravimetric study etc. were performed to affirm the formation of both nanoceria along with drug encapsulated nanoceria.ResultsBoth of these as-prepared formulations inhibited the growth of Gram-positive as well as Gram-negative bacteria confirmed by Disk diffusion study; exhibiting their antibacterial effect. In-vitro drug release study was carried out in physiological environment both in absence and presence of hydrogen peroxide solution to test the reactive ROS-responsiveness of the drug loaded nanocomposites. It also exhibited faster wound healing in diabetes-induced rats. Therefore, it could successfully lower the amount of serum glucose level, inflammation cytokines, hepatotoxic and oxidative stress markers in diabetic rats as confirmed by various ex vivo tests conducted.ConclusionThus, drug loaded ceria nanoparticles have the potential to heal diabetic wounds successfully and can be considered to be useful for the fabrication of appropriate medicated suppositories beneficial for diabetic foot ulcer treatment in future.     

Marine biological injuries and their medical management: A narrative review

The marine environment can be extremely dangerous, and the harm caused by marine organisms when they contact the human body can be especially harmful, even deadly. Contact includes stings, bites, wounds, and consumption as food. In this article, the characteristics of the common marine biological injuries are summarized, the major marine organisms causing damage in China’s marine waters are described, and injury prevention and treatment methods are discussed.     

Effect of submergence on translocation,starch content and amylolytic activity in deep-water rice

Submergence induces rapid internodal elongation in deep-water rice (Oryza sativa L. cv. Habiganj Aman II). We investigated the metabolic activities which help to support such fast growth. Three days of submergence in water under continuous light led to the mobilization of 65% of the starch from those regions of rice internodes which had been formed prior to submergence. Disappearance of starch was accompanied by a 70-fold enhancement of amylolytic activity. Similar increases in amylolytic activity were detected in response to ethylene and gibberellic acid. Submergence also caused a 26-fold increase in the translocation of newly synthesized photosynthetic assimilates from the leaves to the internodes and younger regions of the culms. These physiological processes are likely to provide the metabolic energy required for internodal elongation in response to submergence.Abbreviation GA₃ gibberellic acid     

抑菌生的研究总结报告

本文报告一种由枯草杆菌制成的生态制剂,并命名为抑菌生(Subtilobiogen)。该制剂对创、烧伤感染有治疗作用。经过安全试验、急性毒性试验、Ames试验和微核试验证明,该制剂是一种无害、无毒和有致突变作用的活菌制剂。抑菌生有膏剂、乳剂及粉剂3种剂型。抑菌生在试管和体内对金黄色葡萄球菌、绿脓杆菌和大肠杆菌均具有抑菌作用。临床观察证明,将抑菌生喷洒在创面上,对浅Ⅱ°度、深Ⅱ°度及混合型烧伤感染均具有明显疗效。实验组(181例)与对照组(174例)相比较,在统计学上具有显著性差异。抑菌生的作用机制,经过初步试验证明,与营养争夺和占位性保护有关,因为枯草杆菌的生长速度超过金黄色葡萄球菌、绿脓杆菌和大肠杆菌的生长速度。