Age-dependent deamidation of glutamine residues in human γS crystallin: deamidation and unstructured regions

Human aging is associated with the deterioration of long-lived proteins. Gradual cumulative modifications to the life-long proteins of the lens may ultimately be responsible for the pronounced alterations to the optical and physical properties that characterize lenses from older people. γS crystallin, a major human lens protein, is known to undergo several age-dependent changes. Using proteomic techniques, a site of deamidation involving glutamine 92 has been characterized and its time course established. The proportion of deamidation increased from birth to teen-age years and then plateaud. Deamidation at this site increased again in the eighth decade of life. There was no significant difference in the extent of deamidation between cataract and age-matched normal lenses. Gln92 is located in the linker region between the two domains, and the introduction of a negative charge at this site may alter the interaction between the two regions of the protein. Gln170, which is located in another unstructured part of γS crystallin, showed a similar deamidation profile to that of Gln92. As the other Gln residues in β-sheet regions of γS crystallin appear to remain as amides, modification of Gln92 and Gln170 thus conforms to a pattern whereby deamidation is localized to the unstructured regions of long-lived proteins.     

Accumulation of aluminum in rat brain: does it lead to behavioral and electrophysiological changes?

The present study was undertaken to examine possible aluminum (Al) accumulation in the brain of rats and to investigate whether subchronic exposure to the metal leads to behavioral and neurophysiological changes in both treated and control groups. Each of the groups consisted of 10 animals. Aluminum chloride (AlCl₃) at a low (50 mg/kg/d) or high (200 mg/kg/d) dose was applied to male Wistar rats by gavage for 8 wk. Al-free water by gavage was given to the control group throughout the experiment. Behavioral effects were evaluated by open-field (OF) motor activity and by acoustic startle response (ASR). Electrophysiological examination was done by recording spontaneous activity and sensory-evoked potentials from the visual, somatosensory, as well as auditory cortex. The Al content of each whole brain was determined by electrothermal atomic absorption spectrophotometry. Subchronic Al exposure slightly caused some changes in the evoked potentials and electrocorticograms and in the OF and ASR performance, but these results were not statistically significant. The brain Al levels of the control and the low and high dose of Al-exposed groups were measured as 0.717±0.208 μg/g (wet weight), 0.963±0.491 μg/g (wet weight) and 1.816±1.157 μg/g (wet weight), respectively.     

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more‐individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual‐based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more‐individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS‐curve has the potential to quantify the underlying factors influencing most aspects of diversity change.     

Lens β-crystallins: The role of deamidation and related modifications in aging and cataract

Crystallins are the major proteins in the lens of the eye and function to maintain transparency of the lens. Of the human crystallins, α, β, and γ, the β-crystallins remain the most elusive in their structural significance due to their greater number of subunits and possible oligomer formations. The β-crystallins are also heavily modified during aging. This review focuses on the functional significance of deamidation and the related modifications of racemization and isomerization, the major modifications in β-crystallins of the aged human lens. Elucidating the role of these modifications in cataract formation has been slow, because they are analytically among the most difficult post-translational modifications to study. Recent results suggest that many amides deamidate to similar extent in normal aged and cataractous lenses, while others may undergo greater deamidation in cataract. Mimicking deamidation at critical structural regions induces structural changes that disrupt the stability of the β-crystallins and lead to their aggregation in vitro. Deamidations at the surface disrupt interactions with other crystallins. Additionally, the α-crystallin chaperone is unable to completely prevent deamidated β-crystallins from insolubilization. Therefore, deamidation of β-crystallins may enhance their precipitation and light scattering in vivo contributing to cataract formation.     

HLA-DQ system and insulin-dependent diabetes mellitus in Japanese: does it contribute to the development of IDDM as it does in Caucasians?

Fifty-six unrelated Japanese patients with insulin-dependent diabetes mellitus (IDDM) were HLA-typed, and restriction fragment length polymorphism (RFLP) analysis was performed after enzyme digestion with Bam HI and Taq I by using both DR and DQ probes. As previously reported, increased frequencies of Bw54, Cw1, DR4, and DRw53, which are in strong linkage disequilibrium in the Japanese population and make the characteristic Japanese haplotype, were confirmed. DQw4, a new allele of the DQ system recognized by the monoclonal antibody HU-46 and in linkage disequilibrium with this haplotype, presented the highest IDDM association. The RFLP analysis also showed the strongest correlation to IDDM when the DQ probe was applied. These results indicate that HLA-DQ might play the most important role in the development of IDDM in Japanese as well as in Caucasians. The correlation of DQ amino acid sequences strongly associated with IDDM in Japanese are discussed in this study, and contrasting results were found when such sequences were compared with those of Caucasians.Abbreviations used in this paper IDDM insulin-dependent diabetes mellitus - RFLP restriction fragment length polymorphism - Asp aspartic acid - Asp-57 aspartic acid at the 57th residue of the DQ chain - non-Asp-57 nonaspartic acid at the 57th residue of the DQ chain - R.R. relative risk of Woolf and Haldane     

Toxicity and utilization of chemical weapons: does toxicity and venom utilization contribute to the formation of species communities?

Toxicity and the utilization of venom are essential features in the ecology of many animal species and have been hypothesized to be important factors contributing to the assembly of communities through competitive interactions. Ants of the genus Monomorium utilize a variety of venom compositions, which have been reported to give them a competitive advantage. Here, we investigate two pairs of Monomorium species, which differ in the structural compositions of their venom and their co‐occurrence patterns with the invasive Argentine ant. We looked at the effects of Monomorium venom toxicity, venom utilization, and aggressive physical interactions on Monomorium and Argentine ant survival rates during arena trials. The venom toxicity of the two species co‐occurring with the invasive Argentine ants was found to be significantly higher than the toxicity of the two species which do not. There was no correlation between venom toxicity and Monomorium survival; however, three of the four Monomorium species displayed significant variability in their venom usage which was associated with the number of Argentine ant workers encountered during trials. Average Monomorium mortality varied significantly between species, and in Monomorium smithii and Monomorium antipodum, aggressive interactions with Argentine ants had a significant negative effect on their mortality. Our study demonstrates that different factors and strategies can contribute to the ability of a species to withstand the pressure of a dominant invader at high abundance, and venom chemistry appears to be only one of several strategies utilized.     

Mössbauer spectroscopy of the iron cores in human liver ferritin, ferritin in normal human spleen and ferritin in spleen from patient with primary myelofibrosis: preliminary results of comparative analysis

Comparative study of human liver ferritin and spleen tissues from healthy human and patient with primary myelofibrosis was carried out using Mössbauer spectroscopy with a high velocity resolution at 295 and 90 K and with a low velocity resolution at 20 K. The results obtained demonstrated that the iron content in patient’s spleen in the form of iron storage proteins was about ten times larger than that in normal tissue. However, in the case of patient with primary myelofibrosis the magnetic anisotropy energy barrier differed from that in normal case and, probably, the iron core size was supposed to be slightly larger than that in both normal spleen tissue and normal human liver ferritin in contrast to well-known data for iron overload in patients with thalassemia accompanied by the iron-core size increase. Therefore, the iron overload in the case of patient with primary myelofibrosis may be related to increase in the ferritin content mainly. It was also found that Mössbauer hyperfine parameters for normal and patient’s spleen and normal human liver ferritin demonstrated some small differences related, probably, to some small structural variations in the ferritin iron cores of patient’s spleen.     

Acetylation of αA-crystallin in the human lens: Effects on structure and chaperone function

α-Crystallin is a major protein in the human lens that is perceived to help to maintain the transparency of the lens through its chaperone function. In this study, we demonstrate that many lens proteins including αA-crystallin are acetylated in vivo. We found that K70 and K99 in αA-crystallin and, K92 and K166 in αB-crystallin are acetylated in the human lens. To determine the effect of acetylation on the chaperone function and structural changes, αA-crystallin was acetylated using acetic anhydride. The resulting protein showed strong immunoreactivity against a N^ε-acetyllysine antibody, which was directly related to the degree of acetylation. When compared to the unmodified protein, the chaperone function of the in vitro acetylated αA-crystallin was higher against three of the four different client proteins tested. Because a lysine (residue 70; K70) in αA-crystallin is acetylated in vivo, we generated a protein with an acetylation mimic, replacing Lys70 with glutamine (K70Q). The K70Q mutant protein showed increased chaperone function against three client proteins compared to the Wt protein but decreased chaperone function against γ-crystallin. The acetylated protein displayed higher surface hydrophobicity and tryptophan fluorescence, had altered secondary and tertiary structures and displayed decreased thermodynamic stability. Together, our data suggest that acetylation of αA-crystallin occurs in the human lens and that it affects the chaperone function of the protein.     

Can human embryonic stem cells contribute to the discovery of safer and more effective drugs?

Few scientific achievements have received such irresistible attention from scientists, clinicians, and the general public as the ability of human embryonic stem (hES) cells to differentiate into functional cell types for regenerative medicine. The most immediate benefit of neurons, cardiomyocytes, and insulin-secreting cells derived from hES cells, however, may reside in their application in drug discovery and toxicology. The availability of renewable human cells with functional similarities to their in vivo counterparts is the first landmark for a new generation of cell-based assays. The development of cell-based assays using human cells that are physiological targets of drug activity will increase the robustness of target validation and efficacy, high-throughput screening (HTS), structure-activity relationship (SAR), and should introduce safer drugs into clinical trials and the marketplace. The pluripotency of embryonic stem cells, that is, the capacity to generate multiple cell types, is a novel path for the discovery of 'regenerative drugs', the pursuit of small molecules that promote tissue repair (neurogenesis, cardiogenesis) or proliferation of resident stem cells in different organs, thus creating drugs that work by a novel mechanism.     

How does landscape context contribute to effects of habitat fragmentation on diversity and population density of butterflies?

Aim Studies on habitat fragmentation of insect communities mostly ignore the impact of the surrounding landscape matrix and treat all species equally. In our study, on habitat fragmentation and the importance of landscape context, we expected that habitat specialists are more affected by area and isolation, and habitat generalists more by landscape context. Location and methods The study was conducted in the vicinity of the city of Göttingen in Germany in the year 2000. We analysed butterfly communities by transect counts on thirty‐two calcareous grasslands differing in size (0.03–5.14 ha), isolation index (2100–86,000/edge‐to‐edge distance 55–1894 m), and landscape diversity (Shannon–Wiener: 0.09–1.56), which is correlated to percentage grassland in the landscape. Results A total of 15,185 butterfly specimens belonging to fifty‐four species are recorded. In multiple regression analysis, the number of habitat specialist (n = 20) and habitat generalist (n = 34) butterfly species increased with habitat area, but z‐values (slopes) of the species–area relationships for specialists (z = 0.399) were significantly steeper compared with generalists (z = 0.096). Generalists, but not specialists, showed a marginally significant increase with landscape diversity. Effects of landscape diversity were scale‐dependent and significant only at the smallest scale (landscape context within a 250 m radius around the habitat). Habitat isolation was not related to specialist and generalist species numbers. In multiple regression analysis the density of specialists increased significantly with habitat area, whereas generalist density increased only marginally. Habitat isolation and landscape diversity did not show any effects. Main conclusions Habitat area was the most important predictor of butterfly community structure and influenced habitat specialists more than habitat generalists. In contrast to our expectations, habitat isolation had no effect as most butterflies could cope with the degree of isolation in our study region. Landscape diversity appeared to be important for generalist butterflies only.     

Formation of N′-formylkynurenine in proteins from lens and other sources by exposure to sunlight

The photo-oxidative effect of sunlight on the tryptophan residues of proteins and on free tryptophan is described. Evidence is presented that the indole ring is split to yield N'-formylkynurenine. The possible relation of this photo-oxidative change to changes in the lens proteins of brown cataracts is discussed.     

The course of diabetes in children,adolescents and young adults: does the autoimmunity status matter?

Background

Initial classification of diabetes of young may require revision to improve diagnostic accuracy of different forms of diabetes.The aim of our study was to examine markers of beta-cell autoimmunity in a cohort of young (0–25 years) patients with type 1 diabetes and compare the presentation and course of the disease according to the presence of pancreatic antibodies.

Methods

Cross-sectional population-based study was performed covering 100% of pediatric (n?=?860) and 70% of 18–25 years old adult patients (n?=?349) with type 1 diabetes in Lithuania.

Results

No antibodies (GAD65, IA-2, IAA and ICA) were found in 87 (7.5%) cases. Familial history of diabetes was more frequent in those with antibodies-negative diabetes (24.1 vs. 9.4%, p?<?0.001). Gestational age, birth weight and age at diagnosis was similar in both groups. Ketosis at presentation was more frequent in patients with autoimmune diabetes (88.1 vs. 73.5%, p?<?0.05). HbA1c at the moment of investigation was 8.6 (3) vs. 8.7 (2.2)% in antibodies-negative and antibodies-positive diabetes groups, respectively, p?>?0.05. In the whole cohort, neuropathy was found in 8.8% and nephropathy - in 8.1% of cases, not depending on autoimmunity status. Adjusted for age at onset, disease duration and HbA1c, retinopathy was more frequent in antibodies-negative subjects (13.8 vs. 7.8%, p?<?0.05).

Conclusion

Antibodies-negative pediatric and young adult patients with type 1 diabetes in this study had higher incidence of family history of diabetes, higher frequency of retinopathy, less frequent ketosis at presentation, but similar age at onset, HbA1c, incidence of nephropathy and neuropathy compared to antibodies-positive patients.

     

From species to individuals: does the variation in ant–plant networks scale result in structural and functional changes?

Predicting the outcomes of any mutualistic interaction between ants and plants can be a very difficult task, since these outcomes are often determined by the ecological context in which the interacting species are embedded. Network theory has been an important tool to improve our understanding about the organizational patterns of animal–plant interactions. Nevertheless, traditionally, network studies have focused mainly on species-based differences and ignoring the importance of individual differences within populations. In this study, we evaluated if downscaling an ant–plant network from species to the individual level results in structural and functional changes in a network involving different-sized plant individuals. For this, we studied the extrafloral-nectar producing-tree Caryocar brasiliense (Caryocaraceae) and their associated ants in a Neotropical savanna. We observed 254 interactions involving 43 individuals of C. brasiliense and 47 ant species. The individual-based ant–plant network exhibited a nested pattern of interactions, with all developmental stages contributing equally to structuring this non-random pattern. We also found that plants with greater centrality within the network were better protected by their ant partners. However, plants with higher levels of individual specialization were not necessarily better protected by ants. Overall, we presented empirical evidence that intra-population variations are important for shaping ant–plant networks, since they can change the level of protection against herbivores conferred by the ants. These results highlight the importance of individual-based analyses of ecological networks, opening new research venues in the eco-evolutionary dynamics of ant–plant interactions.     

Will family studies return to prominence in human genetics and genomics? Rare variants and linkage analysis of complex traits

A major focus of modern human genetics has been the search for genetic variations that contribute to human disease. These studies originated in families and used linkage methods as a primary analytical tool. With continued technical improvements, these family-based linkage studies have been very powerful in identifying genes contributing to monogenic disorders. When these methods were applied to disorders with complex, non-Mendelian patterns of inheritance they largely failed. The development of effective capabilities for Genome Wide Association Studies (GWAS) relegated family-based studies to a peripheral role in human genetics research. Despite the remarkable record of GWAS discoveries, common variations identified in GWAS account for a limited (frequently less than 10%) proportion of the heritable risk of qualitative traits or variance of quantitative traits. Next generation sequencing is facilitating a re-examination of family-based methods with surprising and intriguing results. We propose that rare variants of large effect underlie many linkage peaks, including complex quantitative phenotypes, and review the issues underlying this proposed basis for complex traits.     

Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

Background  

The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs) has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%.