积水和网孔大小对青藏高原高寒沼泽化草甸优势种黑褐苔草叶片凋落物早期分解的影响

2013年5月,在青藏高原高寒沼泽化草甸收集优势种黑褐苔草(Carex atrofusca)立枯体凋落物。6月初,选择3个样带:长期积水带、周期性积水带和无积水带,并结合凋落物分解袋的方法,在每个样带区设置网孔大小分别为大(4.5 mm)、中(2.0 mm)、小(0.1mm)的3种凋落物分解袋,研究积水状态和网孔大小对凋落物早期分解的影响。结果显示:长期积水显著抑制凋落物的分解,而周期性积水和无积水环境中凋落物的质量损失率在大、中、小网孔凋落物袋中没有显著性的差异;网孔显著影响凋落物质量损失率,表现为大网孔中网孔小网孔;在早期分解过程中,凋落物的氮、磷均表现为富集;积水状态显著影响凋落物分解后氮、磷的富集;网孔大小对凋落物氮富集的影响显著,而对磷富集的影响不显著;积水状态和网孔大小对凋落物氮富集影响的交互作用极显著,但对磷富集没有显著的交互作用。研究发现,积水状态和网孔大小影响高寒沼泽化草甸凋落物分解以及氮、磷养分动态,由于不同网孔对凋落物分解的影响可用来反映不同土壤生物对凋落物分解的影响,因此,积水和土壤生物对维持高寒沼泽化草甸生态系统的结构和功能起着非常重要的作用。     

Long‐term change in a behavioural trait: truncated spawning distribution and demography in Northeast Arctic cod

Harvesting may be a potent driver of demographic change and contemporary evolution, which both may have great impacts on animal populations. Research has focused on changes in phenotypic traits that are easily quantifiable and for which time series exist, such as size, age, sex, or gonad size, whereas potential changes in behavioural traits have been under‐studied. Here, we analyse potential drivers of long‐term changes in a behavioural trait for the Northeast Arctic stock of Atlantic cod Gadus morhua, namely choice of spawning location. For 104 years (1866–1969), commercial catches were recorded annually and reported by county along the Norwegian coast. During this time period, spawning ground distribution has fluctuated with a trend towards more northerly spawning. Spawning location is analysed against a suite of explanatory factors including climate, fishing pressure, density dependence, and demography. We find that demography (age or age at maturation) had the highest explanatory power for variation in spawning location, while climate had a limited effect below statistical significance. As to potential mechanisms, some effects of climate may act through demography, and explanatory variables for demography may also have absorbed direct evolutionary change in migration distance for which proxies were unavailable. Despite these caveats, we argue that fishing mortality, either through demographic or evolutionary change, has served as an effective driver for changing spawning locations in cod, and that additional explanatory factors related to climate add no significant information.     

Hip circumduction is not a compensation for reduced knee flexion angle during gait

It has long been held that hip abduction compensates for reduced swing-phase knee flexion angle, especially in those after stroke. However, there are other compensatory motions such as pelvic obliquity (hip hiking) that could also be used to facilitate foot clearance with greater energy efficiency. Our previous work suggested that hip abduction may not be a compensation for reduced knee flexion after stroke. Previous study applied robotic knee flexion assistance in people with post-stroke Stiff-Knee Gait (SKG) during pre-swing, finding increased abduction despite improved knee flexion and toe clearance. Thus, our hypothesis was that hip abduction is not a compensation for reduced knee flexion. We simulated the kinematics of post-stroke SKG on unimpaired individuals with three factors: a knee orthosis to reduce knee flexion, an ankle-foot orthosis commonly worn by those post-stroke, and matching gait speeds. We compared spatiotemporal measures and kinematics between experimental factors within healthy controls and with a previously recorded cohort of people with post-stroke SKG. We focused on frontal plane motions of hip and pelvis as possible compensatory mechanisms. We observed that regardless of gait speed, knee flexion restriction increased pelvic obliquity (2.8°, p < 0.01) compared to unrestricted walking (1.5°, p < 0.01), but similar to post-stroke SKG (3.4°). However, those with post-stroke SKG had greater hip abduction (8.2°) compared to unimpaired individuals with restricted knee flexion (4.2°, p < 0.05). These results show that pelvic obliquity, not hip abduction, compensates for reduced knee flexion angle. Thus, other factors, possibly neural, facilitate exaggerated hip abduction observed in post-stroke SKG.     

Towards predicting Ca2+‐binding sites with different coordination numbers in proteins with atomic resolution

Ca²⁺‐binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally‐diverse set of biological functions. Although the highly‐conserved EF‐Hand motif has been studied extensively, non‐EF‐Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca²⁺‐binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca²⁺‐binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca²⁺‐binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca²⁺ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca²⁺ positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca²⁺‐binding sites in three datasets of highly‐diversified protein structures with 0.22 to 0.49 Å accuracy. All multiple‐binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low‐coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor‐coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low‐coordination and cofactor‐coordinating Ca²⁺‐binding sites. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Diversification in flowering time due to tandem FT-like gene duplication, generating novel Mendelian factors in wild and cultivated rice

The complex structure of a single Mendelian factor widespread in the Asian cultivated rice ( Oryza sativa ) and its wild progenitor ( Oryza rufipogon ) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se-pat gene. Fine mapping in two of these near-isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly-observed recessive gene ( se-pat ). Molecular dissection suggested that the tandemly duplicated FT-like genes ( Hd3a and RFT1 ) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype × environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se-pat ⁺ alleles might have emerged in different lineages within O. sativa . The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.