Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design

Improving the affinity of a high-affinity protein-protein interaction is a challenging problem that has practical applications in the development of therapeutic biomolecules. We used a combination of structure-based computational methods to optimize the binding affinity of an antibody fragment to the I-domain of the integrin VLA1. Despite the already high affinity of the antibody (Kd approximately 7 nM) and the moderate resolution (2.8 A) of the starting crystal structure, the affinity was increased by an order of magnitude primarily through a decrease in the dissociation rate. We determined the crystal structure of a high-affinity quadruple mutant complex at 2.2 A. The structure shows that the design makes the predicted contacts. Structural evidence and mutagenesis experiments that probe a hydrogen bond network illustrate the importance of satisfying hydrogen bonding requirements while seeking higher-affinity mutations. The large and diverse set of interface mutations allowed refinement of the mutant binding affinity prediction protocol and improvement of the single-mutant success rate. Our results indicate that structure-based computational design can be successfully applied to further improve the binding of high-affinity antibodies.     

Pathogenicity of the pinewood nematode, Bursaphelenchus xylophilus, to Japanese larch, Larix kaempferi, seedlings

Pathogenicity of the pine wood nematode, Bursaphelenchus xylophilus, to Japanese larch, Larix kaempferi, seedlings was tested with inoculation experiments under nursery conditions. Water suspensions of nematodes (mixed stages cultured on Botrytis cinerea or dispersal fourth-stage juveniles (DJ4) extracted from the adult Japanese pine sawyer, Monochamus alternatus) were injected into the stems of 2- and 3-year-old Japanese larch and Japanese black pine, Pinus thunbergii, seedlings growing in a nursery. In another treatment, Japanese pine sawyer adults holding DJ4 were released under a net that covered the upper half of the seedlings. Regardless of nematode inoculation method, Japanese larch seedlings were as susceptible as Japanese black pine seedlings to B. xylophilus under nursery conditions. The rate of disease development was similar on larch and pine seedlings. Nematode population densities were lower in the stems of dead larch seedlings than in the stems of dead pine seedlings. Histopathological observations revealed that the distribution of nematodes in the stems of dead larch seedlings was mostly limited to the cortex, phloem and cambial zone. Traumatic resin canal formation was one of the most characteristic symptoms in larch seedlings which was dissimilar to that in pine seedlings.     

Redescription of †Paralycoptera wui Chang & Chou, 1977 (Teleostei: Osteoglossoidei) from the Early Cretaceous of eastern China

?Paralycoptera wui Chang & Chou, 1977 from the Early Cretaceous of China is redescribed herein through a re‐examination of the original materials, as well as observations on some newly collected specimens. The use of the peeling method has revealed much of the new or revised information on its osteology, e.g. aspects of the nasal, infraorbitals, retroarticular, preopercle, extrascapular, basihyal toothplate, epineural, pelvic fin, caudal skeleton and scales. The phylogenetic relationships of ?Paralycoptera and other osteoglossomorphs are re‐evaluated. The cladistic analysis largely agrees with the previous hypothesis that ?Paralycoptera is not a ?lycopterid, but rather a stem osteoglossoid. ?Paralycoptera is excluded from notopteroids and exhibits the following derived characters of the Osteoglossoidei: (1) palatal area behind and below orbit completely covered by infraorbitals; (2) jaw articulation under posterior portion of orbit; (3) opercle depth twice or more its width; (4) first pectoral fin ray much enlarged and long, extending posteriorly beyond origin of pelvic fin. ?Singida and ?Phareodus are regarded as different levels of osteoglossoids above ?Paralycoptera. ?Singida shares the following derived characters with ?Phareodus plus extant osteoglossoids: (1) jaw articulation posterior to orbit; (2) anterior process of hyomandibula in contact with entopterygoid; (3) subopercle small and anterior to opercle. ?Phareodus shares the following derived characters with extant osteoglossoids: (1) supraorbital and otic sensory canals connected; (2) one uroneural; (3) reticulate furrows present over entire scale.     

Short- and long-term consequences of individual and territory quality in a long-lived bird

Site-quality is a major determinant of fitness but its effect can be confounded by individual quality, a relationship that has been little studied in large, long-lived vertebrates. The fitness effects of quality estimates depend on the assumption of co-variation between individual and territory quality and can be framed as five working hypotheses: no effect on fitness, exclusive effect of individual quality, exclusive effect of site quality, and independent or interactive effects of the two. We explored such a framework using a medium-sized raptor, the black kite Milvus migrans, as a model species. Individual and territory quality co-varied, but the strength of the relationship varied across different estimates of individual quality (age, body size, or mass residuals). Short-term production of fledglings was related to the independent effects of both individual and territory quality. However, longer-term production of recruits was related solely to territory quality. The disappearance of individual quality effects over the long-term may be caused by antagonistic selective pressures acting during different stages of the life cycle. Our results contribute to a growing appreciation of the long-term fitness-benefits of advantages experienced in early life and highlight the importance of a long-term perspective in studies assessing the effects of individual and territory quality. In our case study, prioritizing sites for conservation on the basis of territory quality may be a feasible pathway to maintain the viability of the population. However, scenarios where such a method could be inefficient have been previously reported, suggesting caution in its application. More studies are needed to understand the generality of the efficiency of priority-setting approaches based on site quality.     

GUODUNITES, A LOW-PALAEOLATITUDE AND TRANS-PANTHALASSIC SMITHIAN (EARLY TRIASSIC) AMMONOID GENUS

Abstract:  Based on new, bed-rock controlled material from Oman and Utah, USA, the Early Triassic genus Guodunites , which was recently erected on the basis of scarce specimens from northwestern Guangxi, South China, is now shown to be a representative of Proptychitidae. This solves the question of the previously unknown phylogenetic affinity of this genus. The genus is restricted to the late middle Smithian, and to date, its biogeographical distribution comprises Oman, South China and Utah, thus indicating an essentially low palaeolatitudinal distribution during the Early Triassic. Its palaeobiogeographical distribution further strengthens the existence of significant equatorial faunal exchanges between both sides of the Panthalassa at that time. It also suggests that, in addition to the potential stepping stones represented by Panthalassic terranes, vigorous equatorial oceanic currents must have contributed largely to the dispersal of ammonoids during such time intervals.     

The most ancient terrestrial lichen <Emphasis Type="Italic">Winfrenatia reticulata</Emphasis>: A new find and new interpretation

Silicified fossils from Rhynie cherts in Scotland are studied. A lichen belonging to the genus Winfrenatia is detected and studied. This oldest terrestrial lichen is dated to the Pragian (=Siegenian) of the Early Devonian. New characters of the lichen are described, and their new interpretation is given. The main component of the lichen thallus is a filamentous cyanobacterium (Nostocales). Structures which were interpreted as fungal hyphae are probably hollow sheaths of this cyanobacterium. Mycobiont hyphae develop at the base of the thallus and symbiose with a coccoid cyanobacterium. Thus, Winfrenatia reticulata is a three-parted organism, constituted of a mycobiont and filamentous and coccoid cyanobacteria.     

辽宁早白垩世会鸟一新种(英文)

记述了辽宁朝阳大平房早白垩世九佛堂组湖相地层中发现的会鸟化石一新种,窄脊会鸟(Sapeornis angustis sp.nov.)。尽管新种正型标本属于一亚成年个体,但除个体较小外,还在许多特征上很容易与属型种(朝阳会鸟)相区别。例如,不超过6枚荐椎,肱骨的三角脊和气窗均较细窄,三角脊远端的背突不显著尖锐,乌喙骨具有较长的肩峰突,叉骨枝较细,叉骨突较短,第一掌骨以及耻骨突均相对较短等。和始祖鸟以及其他已报道的会鸟标本一样,新种材料没有保存胸骨,肋骨上也未见钩状突起,推测这两种结构可能在个体发育的晚期才开始骨化,上述标本均为发育早中期的个体。会鸟新种的发现为这一基干的原始鸟类提供了新的解剖特征,并表明在会鸟的演化过程中存在个体的逐步增大以及一些形态特征的特化现象。这一新的发现还为分析早白垩世陆地生态系统的鸟类多样性增添了新的资料。     

广西下泥盆统大瑶山群盔甲鱼类的新发现

广西象州县大乐乡泥盆系剖面是华南象州型(底栖相)泥盆系的标准剖面(侯鸿飞、王士涛,1988),其下部大瑶山群为一套厚达上千米的石英砂岩夹粉砂岩沉积,底部以一层约2 m厚的砾岩与下伏的前泥盆系呈角度不整合接触(白顺良等,1982).     

Overexpression of a Kunitz-type trypsin inhibitor (AtKTI1) causes early flowering in Arabidopsis

An early flowering mutant of Arabidopsis, elf32-D was isolated from activation tagging screening. The mutant flowered earlier than wild type under both long day and short day conditions. The mutant phenotype was caused by overexpression of a Kunitz-type trypsin inhibitor gene (AtKTI1). The expression of AtKTI1 was detected in leaves, flowers, siliques and roots. In the vegetative state, no change of flowering integrator gene expression was observed for AtKTI1 overexpressing plants. In contrast, at the reproductive stage, its overexpression resulted in the down-regulation of FLC, a strong floral repressor which integrates the autonomous and vernalization pathways and also the up-regulation of FT and AP1, which are downstream floral integrator genes. It is probable that the AtKTI1 overexpression inhibits components of the flowering signaling pathway upstream of FLC, eventually regulating expression of FLC, or causing perturbations in plant metabolism and thus indirectly affecting flowering.