pp 569-574 September 2018 Article
The essential role of regular physical activity has been emphasized for maintaining a healthy life. However, unfortunately, duringthe last few decades, the lifestyle of people has led to a decrease in physical activity. Research studies have shown that exercise ofdifferent intensities is applied on reproductive performance indices, luteinizing hormone (LH) and testosterone (T), with differenteffects. Nevertheless, the molecular and cellular mechanisms underlying its function are not completely understood. Therefore,this study aimed to evaluate the role of kisspeptin, neurokinin-B and pro-dynorphin (KNDY) gene-expression changes located inthe upstream of GnRH neurons in transferring the effects of different long-term exercise intensities on male reproductive axis.Twenty-one adult Wistar rats were randomly divided into control, 6-month regular moderate exercise (RME-6) and 6-monthregular intensive exercise (RIE-6). In moderate and intensive exercise groups, rats were treated 5 days a week for 60 min, at 22and 35 m/min, respectively. Finally, the hypothalamic arcuate nucleus was isolated and the relative gene expression of kisspeptin(Kiss1), neurokinin-B (Nkb), pro-dynorphin (Pdyn) and gonadotropin-releasing hormone (Gnrh) genes were measured by realtimepolymerase chain reaction method. The results showed that RIE-6 treatment decreased Gnrh and increased Pdyn mRNAlevels in the arcuate nucleus. Furthermore, although RME-6 treatment decreased Nkb and increased Pdyn mRNA levels, theGnrh mRNAwas not affected. Regarding the Gnrh mRNA levels and serum concentrations of reproductive indices (LH and T),moderate exercise did not impose harmful effects on the hypothalamic–pituitary–gonadal axis than intensive exercise. Thedifferent impacts of diverse long-term exercise intensities on the male pituitary–gonadal axis maybe relay by the various changesin hypothalamic Nkb and Pdyn gene expressions.
pp 575-583 September 2018 Article
5,6-Dihydroxy-5,6-dihydrothymine (thymine glycol) and 7,8-dihydro-8-oxo-20-deoxyguanosine (8-oxodG) are major DNAdamage lesions produced by endogenous oxidative stress, as well as inflicted by carcinogens and ionizing radiation. Theprocessing of Tg:G mismatch and 8-oxodG in close proximity of each other in a bistranded clustered environment in DNAoligomer duplexes as well as in a nucleosome core particle (NCP) model are reported here. The processing of the lesionswas evaluated by purified enzyme cocktails of hNTH1 and hOGG1 as well as with a HeLa cell extract. Interestingly, theyield of double-strand breaks (DSBs) resulting from the processing of the bistranded lesions are appreciably lower when theDNA is treated with the HeLa cell extract compared with the relevant purified enzyme cocktail in both models. Clusteredbistranded lesions become more repair refractive when reconstituted as an NCP. This indicates a complex interplay betweenthe repair enzymes that influence the processing of the bistranded cluster damage positively to avoid the formation of DSBsunder cellular conditions. In addition to position and orientation of the lesions, the type of the lesions in the clusterenvironment in DNA along with the relative abundance of the lesion-specific enzymes in the cells strongly prevents theprocessing of the oxidized nucleobases.
pp 585-596 September 2018 Article
In the present study, the effects of polyphenols on the chemical composition of the hepatopancreas of the Astacusleptodactylus, a highly sought farmed crayfish, have been investigated by attenuated total reflectance–Fourier transforminfrared (ATR-FTIR) spectroscopy. The hepatopancreas spectrum was quite complex and contained several peaks arisingfrom the contribution of different functional groups belonging to protein, lipids and carbohydrates. The PCA statisticalanalysis revealed that there were significant differences between crayfish fed a diet without polyphenols and crayfish fed adiet containing polyphenols. Such differences indicated an increase in lipids and proteins in the hepatopancreas ofpolyphenol-fed crayfish. In conclusion, the analysis of the infrared spectral profile of the hepatopancreas of Astacusleptodactylus, allowed us to elucidate the changes in different biomolecules in response to polyphenol treatment, andconfirms the suitability of ATR-FTIR spectral data to analyze diet-induced metabolic effects. These considerations, coupledwith the small amount of sample and no preparation needed, make ATR-FTIR a useful tool for routine analyses where themetabolic impact of substances is investigated, especially with a large number of samples.
pp 597-604 September 2018 Article
Mycobacterium tuberculosisitalic> H37Rv is an intracellular pathogen responsible for causing tuberculosis in humans. The M.tuberculosisitalic> genome has been shown to contain a very large and unique family of PE proteins made of two sub-families:PE-only and PE_PGRS proteins. These two subtypes of proteins play a crucial role in the pathogenesis of the microbe.However, despite numerous investigations, the role of these proteins in disease development remains obscure. In this study,sequence analysis with a search for short conserved motifs revealed a conserved tetra-peptide motif DEVS/DXXS at the PEdomain of almost every PE-only and PE_PGRS protein. The motif was found at a distance of 43–46 amino acids from theN-terminal of PE_PGRS proteins, and at a distance of between 35 and 82 amino acids of the PE-only proteins. Asphosphorylation of the serine residue of this tetra-peptide could yield a motif similar to the caspase-3 binding recognitionsequence DEVD/E, the region from a representative PE_PGRS protein (PE_PGRS45) was docked to human caspase-3.Strong interactions of only the protein containing the phosphorylated motif (DEVpS/DXXpS) to caspase-3 were observed.This suggested that the conserved DEVS/DXXS motif could have evolved for phosphorylation and subsequent recognitionby caspase-3. These findings have important implications in unravelling the role of these PE proteins in mycobacterialinfection.
pp 605-619 September 2018 Article
In vertebrates, early developing epidermis is a bilayered epithelium consisting of an outer periderm and the underlying basalepidermis. It eventually develops into a multi-layered epithelium. The mechanisms that control the architecture andhomeostasis of early developing bilayered epidermis have remained poorly understood. Recently, we have shown that thefunction of Myosin Vb, an actin based molecular motor, is essential in peridermal cells for maintenance of plasmamembrane homeostasis. Furthermore, our analyses of the goosepimples/myosin Vb mutant unravelled a direct link betweenplasma membrane homeostasis, cell size maintenance and tissue homeostasis in the developing epidermis. However, itremained unclear whether this link is specific to myosin Vb mutant or this is a general principle. Here we have identified twomore genetic conditions, romeharsha mutant and clint1 knockdown, in which membrane homeostasis is perturbed, asevident by increased endocytosis and accumulation of lysosomes. As a consequence, peridermal cells exhibit smaller sizeand increased proliferation. We further show that decreasing endocytosis in romeharsha mutant and clint1 morphantsrescues or mitigates the effect on cell size, cell proliferation and morphological phenotype. Our data confirms generality ofthe principle by reaffirming the causal link between plasma membrane homeostasis, cell size maintenance and tissuehomeostasis.
pp 621-633 September 2018 Article
Nuclear Matrix (NuMat) is the structural and functional framework of the nucleus. It has been shown that attachment ofchromatin to NuMat brings significant regulation of the transcriptional activity of particular genes; however, key componentsof NuMat involved in this process remain elusive. We have identified Lid (Little imaginal discs) as one of thecomponents of NuMat. It belongs to the TrxG group of proteins involved in activation of important developmental genes.However, unlike other activator proteins of TrxG, Lid is a Jumonji protein involved in H3K4me3 demethylation. Here, wereport the association of Lid and its various domains with NuMat which implicates its structural role in chromatinorganization and epigenetic basis of cellular memory. We have found that both N and C terminal regions of this protein arecapable of associating with NuMat. We have further mapped the association of individual domains and found that, PHD,ARID and JmjC domains can associate with NuMat individually. Moreover, deletion of N-terminal PHD finger does notalter Lid’s NuMat association implying that although it is sufficient, yet, it is not necessary for Lid’s structural role inNuMat. Based on our findings, we hypothesize that C terminal region of Lid which contains PHD fingers might beresponsible for its NuMat association via protein–DNA interactions. However, for the N terminal region harboring both aPHD and an ARID finger, Lid anchors to the NuMat via both protein-protein and protein-DNA interactions. The associationof JmjC domain with NuMat is the first report of the association of a demethylase domain with NuMat suggesting that Lid,a demethylase, being part of NuMat might be involved in regulating the chromatin dynamics via its NuMat association.
pp 635-648 September 2018 Article
Depletion of oxygen in certain marine areas creates oxygen minimum zones (OMZs), which can alter the species compositionand abundance. We have carried out high-throughput 16S rRNA gene amplicon profiling from the Bay of Bengal(BOB) OMZ and non-OMZ areas. Typically, a total of 35 families of micro-organisms were identified as biomarkers forOMZ and non-OMZ regions in the BOB. Our analysis has identified families Pseudoalteromonadaceae, OM60 andSynechococcaceae to be abundant in oxygenated water, whereas organisms belonging to families Pelagibacteraceae andCaulobacteraceae, which are involved in sulphur and nitrogen metabolism, were prominent in the OMZ areas. Predictivefunctional analysis for these identified bacteria clearly that suggested an abundance of microbes with assimilatory sulphurreducinggenes (cysl and csH) in the non-OMZ, while bacteria involved in dissimilatory sulphate reduction (known to carryaprA and aprB genes) were enriched in the OMZ areas. Comparative analysis with OMZ areas from Peru and Chilerevealed that OMZ areas in the BOB are characterized by specific and distinctive bacterial diversity. Overall, the currentanalysis provides valuable documentation about the bacterial populations and their characteristics, which can generatepointers for their functional significance in the BOB.
pp 649-659 September 2018 Article
Glucose-induced oxidative stress in the diabetic pancreas directly affects viability and the consequent therapeutic outcomeof transplanted stem cells. Pretreatment of stem cells with growth factors induces tolerance in them against various stresses(hypoxia, thermal or hyperglycaemic). This study investigated the effect of pretreatment on insulin-producing cells (IPCs)differentiated from adipose-derived mesenchymal stem cells (ADMSCs), with a combination of stromal cell-derived factor1 alpha (SDF1a) and basic fibroblast growth factor (bFGF) against hyperglycaemic stress (17 or 33 mM glucose). Theresults showed that IPCs pretreated with a combination of SDF1a and bFGF exhibited maximally alleviated apoptosis,senescence and cell damage with a concomitantly increased release of insulin, enhanced cell proliferation and greater upregulationof Insulin 1, Insulin 2, Ngn3, Pdx1 and Nkx6.2 when stressed with 33 mM glucose. These findings may offer animproved therapeutic outcome for the treatment of diabetes.
pp 661-671 September 2018 Article
The B7-H4 molecule, a unique negative regulator of T lymphocytes which is overexpressed on the surface of various tumorcells, is a particularly important target candidate for tumor therapy because it can be blocked with anti-B7-H4 antibodies toinhibit the B7-H4 signaling pathway. Our previous work established an anti-B7-H4 single-chain variable fragment (scFv)library, so we have now amplified the genes encoding anti-B7-H4-scFv and human IgG1 CH3 and ligated them by overlapextension PCR to obtain a recombinant gene. After sequencing, the gene was cloned into the expression vector pET43.1aand expression was induced in E. coli BL21 (DE3) by isopropyl-b-D-1-thiogalactopyranoside (IPTG). The protein waspurified on a nickel-nitrilotriacetic acid (Ni-NTA) resin column and its antigen specificity and affinity were examined byELISA and western blotting. We also established a Lewis lung cancer model in C57BL/6 mice to further identify thebiological function of the scFv protein in vivo. The results showed that tumor volume, body weight and necrotic tissues inthe control group were significantly greater than in the experimental group, indicating that selected scFvs had goodbiological activity and could inhibit tumor growth in tumor-bearing mice. Our work thus offers a new approach for thedevelopment of cancer-targeted therapy.
pp 673-684 September 2018 Article
Butterflies and moths possess diverse patterns on their wings. Butterflies employ miscellaneous colour in the wings whereasmoths use a combination of dull colours like white, grey, brown and black for the patterning of their wings. The exception issome of the toxic diurnal moths which possess bright wing colouration. Moths possess an obscure pattern in the dorsal partof the wings which may be a line, zigzag or swirl. Such patterns help in camouflage during resting period. Thus, the dorsalwing pattern of the moth is used for both intra- as well as inter-specific signal communication. Chiasmia eleonora is anocturnal moth of greyish black colouration. The dorsal hindwing possesses yellow and black colour patches. A whitecolouredoblique line crosses both left and right fore- and hindwings to form a V-shaped pattern across the dorsal wing. ThisV-shaped pattern possesses a UV signal. Closer to the body, the colour appears darker, which fades towards the margin. Thefine nanostructural variation is observed throughout the wings. This study elucidates the wing pattern of the geometrid mothC. eleonora using high-resolution microscopy techniques that has not been described in previous studies.
pp 685-691 September 2018 Article
RNA binding proteins (RBPs) can regulate the stability and/or translatability of messengerRNAs (mRNAs) throughinteractions with their 30-untranslated regions. However, individual mRNAs may be regulated simultaneously or successivelyby more than one RBP, as well as by Argonaute (AGO)-bound miRNAs; the coordination of these various influenceson an individual mRNA is therefore complex and not well studied. In this report we examine the roles of two RBPs thatbind to AU-rich elements (ARE) – AUF1 and HuR – in the stability and translation of cyclin D1 (Ccnd1) mRNA in ratmyoblasts transiting the G phase of the cell cycle, and their interactions with miRNAs. Knockdown (KD) of AUF1 resultedin (1) transient upregulation of the mRNA level as well as an advancement of translation onset time (TOT) from 6 to 5 hpost-serum addition, (2) loss of miRNA loading on AGO1 and AGO2 and (3) reduction in the level of AGO-1 and AGO-2bound mRNA. In contrast, KD of HuR had no effect on the mRNA level, or on the AGO–mRNA complexes, but delayedTOT by 1 h independent of miRNA let-7. Thus the dynamics of RBP–mRNA binding and –RBP–AGO–miRNA interactionsare coordinated to fine tune the expression of Ccnd1 in the G1 phase.
pp 693-706 September 2018 Article
Nuclear envelope morphology protein 1 (NEM1) along with a phosphatidate phosphatase (PAH1) regulates lipid homeostasisand membrane biogenesis in yeast and mammals. We investigated four putative NEM1 homologues (TtNEM1A,TtNEM1B, TtNEM1C and TtNEM1D) in the Tetrahymena thermophila genome. Disruption of TtNEM1B, TtNEM1C orTtNEM1D did not compromise normal cell growth. In contrast, we were unable to generate knockout strain of TtNEM1Aunder the same conditions, indicating that TtNEM1A is essential for Tetrahymena growth. Interestingly, loss of TtNEM1Bbut not TtNEM1C or TtNEM1D caused a reduction in lipid droplet number. Similar to yeast and mammals, TtNem1B ofTetrahymena exerts its function via Pah1, since we found that PAH1 overexpression rescued loss of Nem1 function.However, unlike NEM1 in other organisms, TtNEM1B does not regulate ER/nuclear morphology. Similarly, neitherTtNEM1C nor TtNEM1D is required to maintain normal ER morphology. While Tetrahymena PAH1 was shown tofunctionally replace yeast PAH1 earlier, we observed that Tetrahymena NEM1 homologues did not functionally replaceyeast NEM1. Overall, our results suggest the presence of a conserved cascade for regulation of lipid homeostasis andmembrane biogenesis in Tetrahymena. Our results also suggest a Nem1-independent function of Pah1 in the regulation ofER morphology in Tetrahymena.
pp 707-715 September 2018 Article
Antibiotic resistance in bacteria is a major health concern. Antimicrobial peptides (AMPs) are a class of peptides that areefficient in killing most microbes yet development of resistance to AMPs is rare. However, complex secondary and tertiarystructures and difficulties in isolating AMPs have limited their use as antibiotics. It has been demonstrated earlier that smallpeptides derived from human b defensin-3 (HBD-3) also show antibacterial activity. Here, we perform a detailed characterizationof the antibacterial activity of one such derivative: CHRG01. While HBD-3 has 45 amino acids with threedisulphide bonds and a b-sheet folded structure, CHRG01 has only 14 amino acids with the cysteine residues replaced byserine. The antibacterial nature of CHRG01 was studied using scanning electron microscopy (SEM), confocal microscopy,circular dichroism (CD) and small-angle X-ray scattering (SAXS). CD data show that CHRG01 is random coiled insolution. SEM and confocal studies show that the mode of action of CHRG01 is pore forming. SAXS studies show thatCHRG01 induces a negative Gaussian curvature, the type of curvature needed for pore formation. The above results showthat CHRG01, a small peptide without any complex structure, is capable of killing bacteria by permeabilizing their outermembranes.
pp 717-729 September 2018 Article
Diatoms are photosynthetic unicellular microalgae and are nature’s hidden source of several biosynthetic metabolites withtheir use in biofuel, food and drug industries. They mainly contain various lipids, sterols, isoprenoids and toxins with theiruse in apoptotic, fertility controlling and cancer drugs. Chemical studies on diatoms are limited due to various limitationssuch as variation of nutrients, contaminants and change in seasonal factors in the environment. To overcome theselimitations, we obtained axenic cultures of 12 fresh-water diatom strains on the 22nd day of inoculation having a dry weightof 1 mg each and performed their Fourier transform infrared (FTIR) study for the detection of functional groups responsiblefor their chemical moiety. The spectral mapping showed a varied level of polyunsaturated fatty acids, amides, amines,ketone bodies and esters for their applications in various pharmacological, food and biofuel industries in the exponentialphase of their growth in f/2 media. The FTIR study of the 12 diatom strains showed various similarities in the form of somecommon peak patterns ranging from 3000 to 3600 cm-1 for mO–H absorption. The symmetric stretching vibration frequencyof Diadesmis confervaceae (V2) type species showed different behaviour than others in the spectral region starting from1600 to 1700 cm-1. The absorption between 1500 and 1575 cm-1 reflects the presence of the –N–H group. Infrared (IR)absorptions falling between 1600 and 1700 cm-1 reflect the presence of amide’s mC=O in all species. Placoneis elginensis(V8) type species showed an additional absorption band which is centred around 1735–1750 cm-1 which perhaps reflectsthe presence of ester’s mC=O. Diadesmis confervaceae (V2), Nitzschia palea (V4), Placoneis elginensis (V8), Nitzschiapalea var. debilis (V6), Nitzschia inconspicua (V10), Gomphonema parvulum (V11) and Sellaphora (V12) showed distinctstructural features with important key functionalities that can make them essential drug markers in the pharmaceuticalindustry.
pp 731-738 September 2018 Mini-Review
Tissue analysis in histology is extremely important and also considered to be a gold standard to diagnose and prognosticateseveral diseases including cancer. Intraoperative evaluation of surgical margin of tumor also relies on frozen sectionhistopathology, which is time consuming, challenging and often subjective. Recent development in the ambient ionizationmass spectrometry imaging (MSI) technique has enabled us to simultaneously visualize hundreds to thousands of molecules(ion images) in the biopsy specimen, which are strikingly different and more powerful than the single optical tissue imageanalysis in conventional histopathology. This paper will highlight the emergence of the desorption electrospray ionizationMSI (DESI-MSI) technique, which is label-free, requires minimal or no sample preparation and operates under ambientconditions. DESI-MSI can record ion images of lipid/metabolite distributions on biopsy specimens, providing a wealth ofdiagnostic information based on differential distributions of these molecular species in healthy and unhealthy tissues.Remarkable success of this technology in rapidly evaluating the cancer margin intraoperatively with very high accuracyalso promises to bring this imaging technique from bench to bedside.
pp 739-749 September 2018 Mini-Review
Hypoxia is a complex pathophysiological condition. The physiological and molecular responses to this stress have beenextensively studied. However, the management of its ill effects still poses a challenge to clinicians. MicroRNAs (miRNAs)are short non-coding RNA molecules that control post-transcriptional gene expression. The regulatory role of miRNAs inhypoxic environments has been studied in many hypoxia-related disorders, however a comprehensive compilation andanalysis of all data and the significance of miRNAs in hypoxia adaption is still lacking. This review summarizes themiRNAs related to various hypoxia-related disorders and highlights the computational approaches to study them. Thiswould help in designing novel strategies toward efficient management of hypoxia-related disorders.
pp 751-761 September 2018 Review
Most of avian histone H1 non-allelic subtypes, i.e. eight out of nine, show polymorphic heterogeneity manifested by thepresence of two or three allelic variants formed as a result of amino acid deletion and substitution. In addition, some ofhistone H1 non-allelic subtypes exhibit various allelic complements in different bird species leading to the widening of awhole pool of histone H1 polymorphic variation. A wide range of histone H1 heterogeneity may indicate that the polymorphicvariants can individually modulate some histone H1-dependent cellular processes by showing allele-specificinfluence on chromatin organization and function. Although, the exact way of avian histone H1 allelic variants’ activity isnot known, their structural separateness inferred from biochemical experiments and relationship with some characteristicsof organism functioning disclosed in the genetic studies seem to confirm their importance. The aim of this review is tocharacterize the molecular origin of histone H1 polymorphisms and draw attention to the link between the histone H1polymorphic variants and avian organismal features related to the physiological effects of bird individuals’ living in thenatural and breeding populations.
pp 763-784 September 2018 Review
Since the last decade, a lot of advancement has been made to understand biological processes involving complex intracellularpathways. The major challenge faced was monitoring and trafficking of metabolites in real time. Although a rangeof quantitative and imaging techniques have been developed so far, the discovery of green fluorescent proteins (GFPs) hasrevolutionized the advancement in the field of metabolomics. GFPs and their variants have enabled researchers to ‘paint’ awide range of biological molecules. Fluorescence resonance energy transfer (FRET)-based genetically encoded sensors is apromising technology to decipher the real-time monitoring of the cellular events inside living cells. GFPs and their variants,due to their intrinsic fluorescence properties, are extensively being used nowadays in cell-based assays. This review focuseson structure and function of GFP and its derivatives, mechanism emission and their use in the development of FRET-basedsensors for metabolites.
pp 785-795 September 2018 Review
The human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus claimed to be aetiologically linked to the adultT-cell leukaemia/lymphoma (ATLL) and associated myelopathy/tropical spastic paraparesis (HAM/TSP) besides otherminor pathologies. HTLV-1 infection is worldwide distributed, despite its heterogeneous prevalence. Environmental factorsand host-genetic background are very likely to determine the epidemiological profile of HTLV-1 prevalence and relateddisease confinement in distinct human ethnic populations and geographical coordinates, which raises the question if thevirus is a real pathogen or a runaway well-organized packed genome of a burden host cell near death process. Newmethodological approaches need to be proposed and applied in order to prove or discard the hypotheses emerged in thepresent review.
pp 797-815 September 2018 Review
The nucleobase cation symporter-1 (NCS1) family of secondary active transport proteins comprises over 2500 sequencedmembers from bacteria, archaea, fungi and plants. NCS1 proteins use a proton or sodium gradient to drive inward cellulartransport of purine and pyrimidine nucleobases and nucleosides, hydantoins and related compounds. The structuralorganization, substrate binding residues and molecular mechanism of NCS1 proteins are defined by crystal structures ofsodium-coupled hydantoin transporter, Mhp1. Plant proteins are most closely related to bacterial/archaeal proteins and thedistinct Fur-type and Fcy-type fungal proteins and plant proteins originated through independent horizontal transfers fromprokaryotes. Analyses of 25 experimentally characterized proteins reveal high substrate specificity in bacterial proteins,distinct non-overlapping specificities in Fur-type and Fcy-type fungal proteins and broad specificity in plant proteins.Possible structural explanations are identified for differences in substrate specificity between bacterial proteins, whilstspecificities of other proteins cannot be predicted by simple sequence comparisons. Specificity appears to be speciesspecific and determined by combinations of effects dictated by multiple residues in the major substrate binding site andgating domains. This is an exploratory research review of evolutionary relationships, function and structural organization,molecular mechanism and origins of substrate specificity in NCS1 proteins and avenues of future direction.
pp 817-818 September 2018 Correction