Trimming down a protein structure to its bare foldons: spatial organization of the cooperative unit

Folding of the ribosomal protein S6 is a malleable process controlled by two competing, and partly overlapping, folding nuclei. Together, these nuclei extend over most of the S6 structure, except the edge strand β2, which is consistently missing in the folding transition states; despite being part of the S6 four-stranded sheet, β2 seems not to be part of the cooperative unit of the protein. The question is then whether β2 can be removed from the S6 structure without compromising folding cooperativity or native state integrity. To investigate this, we constructed a truncated variant of S6 lacking β2, reducing the size of the protein from 96 to 76 residues (S6(Δβ2)). The new S6 variant expresses well in Escherichia coli and has a well dispersed heteronuclear single quantum correlation spectrum and a perfectly wild-type-like crystal structure, but with a smaller three-stranded β-sheet. Moreover, S6(Δβ2) displays an archetypical v-shaped chevron plot with decreased slope of the unfolding limb, as expected from a protein with maintained folding cooperativity and reduced size. The results support the notion that foldons, as defined by the structural distribution of the folding nuclei, represent a property-based level of hierarchy in the build-up of larger protein structures and suggest that the role of β2 in S6 is mainly in intermolecular binding, consistent with the position of this strand in the ribosomal assembly.     

The American Avocet (Recurvirostra americana) as a paradigm for adult automimicry

Summary The body of theory concerning life-history strategies predicts that the duration of high-mortality stages should be minimized by natural selection. This is especially applicable to the avian pre-flight stage, during which growth rates typically are rapid. Using the American Avocet (Recurvirostra americana) as a paradigm, I propose a developmental strategy by which young animals can lower their mortality rates by an accelerated (and deceptive) acquisition of adult or adult-like characters. The benefit accrues when predators misidentify the vulnerable young as adults and fail to attack them because adults are much less vulnerable. This strategy, termed adult automimicry, is most likely to occur in precocial species living in open habitats.American Avocets are large, precocial, open-country shorebirds that first fly when about 4–5 weeks old. They develop a juvenal, plumage in their third week that resembles adult breeding plumage in pattern and color, even though plumage details are different. At this time chicks begin using adult foraging techniques and tend to move away rather than hide from potential predators. A few weeks later they acquire a first winter plumage that resembles adult winter plumage. Thus, avocet chicks appear unusually adult-like after their second week. This should make it difficult for distant predators to distinguish flightless chicks from volant adults.     

High-resolution Native-PAGE for membrane proteins capable of fluorescence detection and hydrodynamic state evaluation

An improved native polyacrylamide gel electrophoresis (PAGE) method capable of evaluating the hydrodynamic states of membrane proteins and allowing in-gel fluorescence detection was established. In this method, bis(alkyl) sulfosuccinate is used to provide negative charges for detergent-solubilized membrane proteins to facilitate proper electrophoretic migration without disturbing their native hydrodynamic states. The method achieved high-resolution electrophoretic separation, in good agreement with the elution profiles obtained by size exclusion chromatography. The applicability of in-gel fluorescence detection for tagged green fluorescent protein (GFP) facilitates the analysis of samples without any purification. This method might serve as a general analytical technique for assessing the folding, oligomerization, and protein complex formation of membrane proteins.     

Multiphoton microscopy for the in-situ investigation of cellular processes and integrity in cryopreservation

In this study we demonstrate a new noninvasive imaging method to monitor freezing processes in biological samples and to investigate life in the frozen state. It combines a laser scanning microscope with a computer-controlled cryostage. Nearinfrared (NIR) femtosecond laser pulses evoke the fluorescence of endogenous fluorophores and fluorescent labels due to multiphoton absorption.The inherent optical nonlinearity of multiphoton absorption allows 3D fluorescence imaging for optical tomography of frozen biological material in-situ. As an example for functional imaging we use fluorescence lifetime imaging (FLIM) to create images with chemical and physical contrast.     

Effects of simultaneous infections of endophytic fungi and arbuscular mycorrhizal fungi on the growth of their shared host grass Achnatherum sibiricum under varying N and P supply

Grasses can be infected by endophytic fungi and arbuscular mycorrhizal (AM) fungi simultaneously. Here, we investigated the interactions of a native grass, Achnatherum sibiricum, with both endophytic and AM fungi (Glomus mosseae, GM and Glomus etunicatum, GE) at different nitrogen (N) and phosphorus (P) levels. The results showed that endophyte infection significantly suppressed the colonization rates and spore density of GE, but had no effect on those of GM. Endophyte infection increased shoot biomass regardless of the nutrient conditions. The effects of AM fungi on host growth were dependent on mycorrhizal species. There was no significant interaction between endophytic fungi and GE on host growth; however, a significant interaction between endophytic fungi and GE occurred in total phenolic concentrations and P uptake. As for GM, a significant interaction among endophytic fungi, AM fungi and nutrient availability occurred in shoot growth. Under sufficient N and P conditions, endophyte infection alleviated the detrimental effects of GM colonization on host growth.     

Antibiogram,prevalence of methicillin-resistant and multi-drug resistant Staphylococcus spp. in different clinical samples

Methicillin-resistant Staphylococcus spp. (MRSS) are causing numerous forms of illness in humans ranging from mild to fatal infections. We need to investigate the resistant pattern for different clinical isolates to control the resistance phenomena. This study was designed to provide the resistance pattern of isolated Staphylococcus spp. from various clinical samples in Khartoum State and to elucidate the frequencies of Multidrug-resistant (MDR), Extensively drug-resistant (XDR) and pan-drug resistant (PDR). Two hundred and ten bacterial isolates were from different sources (catheter tip, sputum, vaginal swab, urine, tracheal aspirate, blood, pus, nasal swab, stool, throat swab, pleural fluid, and ear swab). Isolates were identified based on their morphological characters and biochemical reaction. Antibiotics susceptibility screening was performed using twenty-three antibiotics from eighteen classes against all isolated Staphylococcus spp. following the Clinical and Laboratory Standards Institute (CLSI) guideline. The result revealed that out of 63 Gram-positive isolated bacteria, 52 (82.5%) were Staphylococcus spp. with a high incidence of S. aureus 37(71.2%). Out of all Staphylococcus spp., 38 (73.1%) were Methicillin-resistant (MR). The prevalence of MDR was higher in S. aureus (89.2%) than in S. epidermidis (75%). All Staphylococcus spp. displayed resistance to ampicillin and penicillin, while all S. aureus were sensitive to daptomycin and fosfomycin. One isolate was XDR possible PDR, while no PDR was reported in all isolated bacteria. This study provided evidence for the antimicrobial-resistant (AMR) burden in Sudan and highlighted the need for a practical and functional stewardship program to reduce the unreasonable costs of antibiotics.     

Esophageal squamous cell carcinoma and adenocarcinoma in Malaysia – Pooled data from upper gastrointestinal centers in a multiethnic Asian population

BackgroundEsophageal cancer is the sixth leading cause of cancer death worldwide with considerable geographical histological variation There is a paucity of data in esophageal cancer in demographics, histology, and survival among the multi-ethnic Malaysian population. This paper is a review of esophageal cancer epidemiology and survival among esophageal cancer patients from data collected by the Malaysian Upper Gastrointestinal Surgical Society.MethodsThis is a multicenter retrospective observational study of esophageal cancer patients from six upper gastrointestinal surgical centers in Malaysia between 2005 and 2019. Patient characteristics, histological type and stage were compared and survival analyzed.ResultsThere were 820 patients with esophageal cancer included, where 442 (53.9 %) cases had squamous cell carcinoma (SCC) and 378 (46.1 %) had adenocarcinomas (AC). Malays were the predominant ethnicity with AC (66.7 %) while Indians were the ethnic majority (74.6 %) with SCC. Majority of patients (56.8 %) presented as stage IV disease. Overall, the 1-, 3-, and 5-years’ survival were 35.8 %, 13.8 % and 11.0 %, respectively. Surgical resection with curative intent yielded the best 5-year survival (29.4 %). Intervention in stage IV AC yielded superior survival when compared to SCC (median survival, 7.9 months vs 4.8 months; p, 0.018) Our series demonstrated an increase in AC to SCC over the last 15 years.ConclusionsThere was an ethnic preponderance seen between different histology in this region, not previously discussed. An increase in AC was observed over the last 15 years. Late diagnosis seen in most patients imparts poor prognosis as curative surgery affords the best outcome.     

Monitoring the Interaction between β2-Microglobulin and the Molecular Chaperone αB-crystallin by NMR and Mass Spectrometry: αB-CRYSTALLIN DISSOCIATES β2-MICROGLOBULIN OLIGOMERS*

The interaction at neutral pH between wild-type and a variant form (R3A) of the amyloid fibril-forming protein β₂-microglobulin (β2m) and the molecular chaperone αB-crystallin was investigated by thioflavin T fluorescence, NMR spectroscopy, and mass spectrometry. Fibril formation of R3Aβ2m was potently prevented by αB-crystallin. αB-crystallin also prevented the unfolding and nonfibrillar aggregation of R3Aβ2m. From analysis of the NMR spectra collected at various R3Aβ2m to αB-crystallin molar subunit ratios, it is concluded that the structured β-sheet core and the apical loops of R3Aβ2m interact in a nonspecific manner with the αB-crystallin. Complementary information was derived from NMR diffusion coefficient measurements of wild-type β2m at a 100-fold concentration excess with respect to αB-crystallin. Mass spectrometry acquired in the native state showed that the onset of wild-type β2m oligomerization was effectively reduced by αB-crystallin. Furthermore, and most importantly, αB-crystallin reversibly dissociated β2m oligomers formed spontaneously in aged samples. These results, coupled with our previous studies, highlight the potent effectiveness of αB-crystallin in preventing β2m aggregation at the various stages of its aggregation pathway. Our findings are highly relevant to the emerging view that molecular chaperone action is intimately involved in the prevention of in vivo amyloid fibril formation.     

The contested meanings of 'Asian American': racial dilemmas in the contemporary US

This article explores the contested meanings of the ‘Asian American’ concept in the US today. Since its emergence in the late 1960s, ‘Asian American’ has been defined by pan-Asian groups and organizations in the US as a collectivity bound by shared racial interests. Contemporary conditions have sharpened and highlighted the inherent contradictions and ambiguities of this conception of ‘Asian American’ as a racial interest group. Especially important have been the shifts in the composition of the Asian American population that followed the immigration reforms of 1965. Contestations of ‘Asian American’ also reflect larger uncertainties about the meaning of race in the US today, in particular, the nature of racial boundaries and racial disadvantage.     

Army ant invasions reveal phylogeographic processes across the Isthmus of Panama

Female army ants cannot fly, making them very poor dispersers across water barriers. This dependence on terrestrial corridors motivated the investigation by Winston et al. ( 2017 ), published in this issue of Molecular Ecology, into the role of Panamanian isthmus formation in the diversification of Eciton army ants. Complete closure of this isthmus occurred around three million years ago (3 Ma), but it has also been hypothesized that earlier, temporary land connections facilitated additional colonization events between South and Central America over the past 13 million years or more. The phylogenomic and population genomic analyses by Winston et al. ( 2017 ) uncovered multiple incursions of Eciton lineages into Central America between 4 and 7 Ma. Their study contributes to a growing body of evidence arguing that transitory land bridges predating 3 Ma supported substantial intercontinental biotic exchange.