Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema

Genome-wide analysis of sequence divergence patterns in 12 024 human–mouse orthologous pairs reveals, for the first time, that the trends in nucleotide and amino acid substitutions in orthologs of high and low GC composition are highly asymmetric and polarized to opposite directions. The entire dataset has been divided into three groups on the basis of the GC content at third codon sites of human genes: high, medium, and low. High-GC orthologs exhibit significant bias in favor of the replacements, Thr → Ala, Ser → Ala, Val → Ala, Lys → Arg, Asn → Ser, Ile → Val etc., from mouse to human, whereas in low-GC orthologs, the reverse trends prevail. In general, in the high-GC group, residues encoded by A/U-rich codons of mouse proteins tend to be replaced by the residues encoded by relatively G/C-rich codons in their human orthologs, whereas the opposite trend is observed among the low-GC orthologous pairs. The medium-GC group shares some trends with high-GC group and some with low-GC group. The only significant trend common in all groups of orthologs, irrespective of their GC bias, is (Asp)Mouse → (Glu)Human replacement. At the nucleotide level, high-GC orthologs have undergone a large excess of (A/T)Mouse → (G/C)Human substitutions over (G/C)Mouse → (A/T)Human at each codon position, whereas for low-GC orthologs, the reverse is true

Granulometric and facies analysis of Middle–Upper Jurassic rocks of Ler Dome, Kachchh, western India: an attempt to reconstruct the depositional environment

Grain size analysis is an important sedimentological tool used to unravel hydrodynamic conditions, mode of trans- portation and deposition of detrital sediments. For the present study, detailed grain size analysis was carried out in order to decipher the palaeodepositional environment of Middle–Upper Jurassic rocks of the Ler Dome (Kachchh, western India), which is further reinforced by facies analysis. Microtextures were identified as grooves, straight steps and V-shaped pits, curved steps and solution pits suggesting the predominance of chemical solution activity. Grain size statistical parameters (Graphic and Moment parameters) were used to document depositional processes, sedimen- tation mechanisms and conditions of hydrodynamic energy, as well as to discriminate between various depositional environments. The grain size parameters show that most of the sandstones are medium- to coarse-grained, moderately to well sorted, strongly fine skewed to fine skewed and mesokurtic to platykurtic in nature. The abundance of medi- um- to coarse-grained sandstones indicates fluctuating energy levels of the deposition medium and sediment type of the source area. The bivariate plots show that the samples are mostly grouped, except for some samples that show a scattered trend, which is either due to a mixture of two modes in equal proportion in bimodal sediments or good sorting in unimodal sediments. The linear discriminant function analysis is predominantly indicative of turbidity current de- posits under shallow-marine conditions. The C-M plots indicate that the sediments formed mainly by rolling to bottom suspension and rolling condition in a beach subenvironment. Log probability curves show that the mixing between the suspension and saltation populations is related to variable energy conditions

Low cycle fatigue and cyclic plasticity bahaviour of Indian PHWR / AHWR primary piping materials

The integrity assessment of the primary piping components needs to be demonstrated under normal operation cyclic loadings as well as under complex cycling loadings of extreme magnitude as may come during a severe earthquake event. In order to understand material's cyclic plasticity and fatigue ratcheting behaviour, systematic experimental and analytical investigations have been carried out on specimens of SA333Gr.6 carbon steel and SS304LN stainless steel. The materials specification of SA333Gr.6 is same as used in Primary Heat transport (PHT) piping of Pressurized Heavy Water Reactors (PHWRs) and materials specification of SS304LN steel is same as proposed for Indian Advanced Heavy Water Recactor (AHWRs) Main Heat Transport (MHT) piping. The test program included the properties and cyclic plasticity behaviour. The results of these tests have been investigated in detals using few popular finite element cyclic plasticity models to understand and quantify the materials' cyclic plasticity behaviour. The studies revealed the need to modify the Chaboche model to simulate the LCF/cyclic plasticity and ratcheting under different stress/strain amplitude loading conditions. On accounting for modification, the Chaboche model nicely predicted the LCF and ratcheting response for all the tests. The tests, finite element analyses results and their interpretations have been presented in this paper

Large scale synthesis of 2D graphene oxide by mechanical milling of 3D carbon nanoparticles in air

Graphene oxide (GO) is one of the important functional materials. Large-scale synthesis of it is very challenging. Following a simple cost-effective route, large-scale GO was produced by mechanical (ball) milling, in air, of carbon nanoparticles (CNPs) present in carbon soot in the present study. The thickness of the GO layer was seen to decrease with an increase in milling time. Ball milling provided the required energy to acquire the in-plane graphitic order in the CNPs reducing the disorders in it. As the surface area of the layered structure became more and more with the increase in milling time, more and more oxygen of air got attached to the carbon in graphene leading to the formation of GO. An increase in the time of the ball mill up to 5 hours leads to a significant increase in the content of GO. Thus ball milling can be useful to produce large-scale two-dimensional GO for a short time.Comment: 23 pages, 10 figure

The malleable brain: plasticity of neural circuits and behavior: A review from students to students

One of the most intriguing features of the brain is its ability to be malleable, allowing it to adapt continually to changes in the environment. Specific neuronal activity patterns drive long-lasting increases or decreases in the strength of synaptic connections, referred to as long-term potentiation (LTP) and long-term depression (LTD) respectively. Such phenomena have been described in a variety of model organisms, which are used to study molecular, structural, and functional aspects of synaptic plasticity. This review originated from the first International Society for Neurochemistry (ISN) and Journal of Neurochemistry (JNC) Flagship School held in Alpbach, Austria (Sep 2016), and will use its curriculum and discussions as a framework to review some of the current knowledge in the field of synaptic plasticity. First, we describe the role of plasticity during development and the persistent changes of neural circuitry occurring when sensory input is altered during critical developmental stages. We then outline the signaling cascades resulting in the synthesis of new plasticity-related proteins, which ultimately enable sustained changes in synaptic strength. Going beyond the traditional understanding of synaptic plasticity conceptualized by LTP and LTD, we discuss system-wide modifications and recently unveiled homeostatic mechanisms, such as synaptic scaling. Finally, we describe the neural circuits and synaptic plasticity mechanisms driving associative memory and motor learning. Evidence summarized in this review provides a current view of synaptic plasticity in its various forms, offers new insights into the underlying mechanisms and behavioral relevance, and provides directions for future research in the field of synaptic plasticity.Fil: Schaefer, Natascha. University of Wuerzburg; AlemaniaFil: Rotermund, Carola. University of Tuebingen; AlemaniaFil: Blumrich, Eva Maria. Universitat Bremen; AlemaniaFil: Lourenco, Mychael V.. Universidade Federal do Rio de Janeiro; BrasilFil: Joshi, Pooja. Robert Debre Hospital; FranciaFil: Hegemann, Regina U.. University of Otago; Nueva ZelandaFil: Jamwal, Sumit. ISF College of Pharmacy; IndiaFil: Ali, Nilufar. Augusta University; Estados UnidosFil: García Romero, Ezra Michelet. Universidad Veracruzana; MéxicoFil: Sharma, Sorabh. Birla Institute of Technology and Science; IndiaFil: Ghosh, Shampa. Indian Council of Medical Research; IndiaFil: Sinha, Jitendra K.. Indian Council of Medical Research; IndiaFil: Loke, Hannah. Hudson Institute of Medical Research; AustraliaFil: Jain, Vishal. Defence Institute of Physiology and Allied Sciences; IndiaFil: Lepeta, Katarzyna. Polish Academy of Sciences; ArgentinaFil: Salamian, Ahmad. Polish Academy of Sciences; ArgentinaFil: Sharma, Mahima. Polish Academy of Sciences; ArgentinaFil: Golpich, Mojtaba. University Kebangsaan Malaysia Medical Centre; MalasiaFil: Nawrotek, Katarzyna. University Of Lodz; ArgentinaFil: Paid, Ramesh K.. Indian Institute of Chemical Biology; IndiaFil: Shahidzadeh, Sheila M.. Syracuse University; Estados UnidosFil: Piermartiri, Tetsade. Universidade Federal de Santa Catarina; BrasilFil: Amini, Elham. University Kebangsaan Malaysia Medical Centre; MalasiaFil: Pastor, Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Biología Celular y Neurociencia ; ArgentinaFil: Wilson, Yvette. University of Melbourne; AustraliaFil: Adeniyi, Philip A.. Afe Babalola University; NigeriaFil: Datusalia, Ashok K.. National Brain Research Centre; IndiaFil: Vafadari, Benham. Polish Academy of Sciences; ArgentinaFil: Saini, Vedangana. University of Nebraska; Estados UnidosFil: Suárez Pozos, Edna. Instituto Politécnico Nacional; MéxicoFil: Kushwah, Neetu. Defence Institute of Physiology and Allied Sciences; IndiaFil: Fontanet, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Biología Celular y Neurociencia ; ArgentinaFil: Turner, Anthony J.. University of Leeds; Reino Unid

Theory of excited state absorptions in phenylene-based π\pi-conjugated polymers

Within a rigid-band correlated electron model for oligomers of poly-(paraphenylene) (PPP) and poly-(paraphenylenevinylene) (PPV), we show that there exist two fundamentally different classes of two-photon A$_g$ states in these systems to which photoinduced absorption (PA) can occur. At relatively lower energies there occur A$_g$ states which are superpositions of one electron - one hole (1e--1h) and two electron -- two hole (2e--2h) excitations, that are both comprised of the highest delocalized valence band and the lowest delocalized conduction band states only. The dominant PA is to one specific member of this class of states (the mA$_g$). In addition to the above class of A$_g$ states, PA can also occur to a higher energy kA$_g$ state whose 2e--2h component is {\em different} and has significant contributions from excitations involving both delocalized and localized bands. Our calculated scaled energies of the mA$_g$ and the kA$_g$ agree reasonably well to the experimentally observed low and high energy PAs in PPV. The calculated relative intensities of the two PAs are also in qualitative agreement with experiment. In the case of ladder-type PPP and its oligomers, we predict from our theoretical work a new intense PA at an energy considerably lower than the region where PA have been observed currently. Based on earlier work that showed that efficient charge--carrier generation occurs upon excitation to odd--parity states that involve both delocalized and localized bands, we speculate that it is the characteristic electronic nature of the kA$_g$ that leads to charge generation subsequent to excitation to this state, as found experimentally.Comment: Revtex4 style, 2 figures inserted in the text, three tables, 10 page